Science.gov

Sample records for public dna databases

  1. The Genographic Project Public Participation Mitochondrial DNA Database

    PubMed Central

    Behar, Doron M; Rosset, Saharon; Blue-Smith, Jason; Balanovsky, Oleg; Tzur, Shay; Comas, David; Mitchell, R. John; Quintana-Murci, Lluis; Tyler-Smith, Chris; Wells, R. Spencer

    2007-01-01

    The Genographic Project is studying the genetic signatures of ancient human migrations and creating an open-source research database. It allows members of the public to participate in a real-time anthropological genetics study by submitting personal samples for analysis and donating the genetic results to the database. We report our experience from the first 18 months of public participation in the Genographic Project, during which we have created the largest standardized human mitochondrial DNA (mtDNA) database ever collected, comprising 78,590 genotypes. Here, we detail our genotyping and quality assurance protocols including direct sequencing of the mtDNA HVS-I, genotyping of 22 coding-region SNPs, and a series of computational quality checks based on phylogenetic principles. This database is very informative with respect to mtDNA phylogeny and mutational dynamics, and its size allows us to develop a nearest neighbor–based methodology for mtDNA haplogroup prediction based on HVS-I motifs that is superior to classic rule-based approaches. We make available to the scientific community and general public two new resources: a periodically updated database comprising all data donated by participants, and the nearest neighbor haplogroup prediction tool. PMID:17604454

  2. Public participation in genetic databases: crossing the boundaries between biobanks and forensic DNA databases through the principle of solidarity

    PubMed Central

    Machado, Helena; Silva, Susana

    2015-01-01

    The ethical aspects of biobanks and forensic DNA databases are often treated as separate issues. As a reflection of this, public participation, or the involvement of citizens in genetic databases, has been approached differently in the fields of forensics and medicine. This paper aims to cross the boundaries between medicine and forensics by exploring the flows between the ethical issues presented in the two domains and the subsequent conceptualisation of public trust and legitimisation. We propose to introduce the concept of ‘solidarity’, traditionally applied only to medical and research biobanks, into a consideration of public engagement in medicine and forensics. Inclusion of a solidarity-based framework, in both medical biobanks and forensic DNA databases, raises new questions that should be included in the ethical debate, in relation to both health services/medical research and activities associated with the criminal justice system. PMID:26139851

  3. Public participation in genetic databases: crossing the boundaries between biobanks and forensic DNA databases through the principle of solidarity.

    PubMed

    Machado, Helena; Silva, Susana

    2015-10-01

    The ethical aspects of biobanks and forensic DNA databases are often treated as separate issues. As a reflection of this, public participation, or the involvement of citizens in genetic databases, has been approached differently in the fields of forensics and medicine. This paper aims to cross the boundaries between medicine and forensics by exploring the flows between the ethical issues presented in the two domains and the subsequent conceptualisation of public trust and legitimisation. We propose to introduce the concept of 'solidarity', traditionally applied only to medical and research biobanks, into a consideration of public engagement in medicine and forensics. Inclusion of a solidarity-based framework, in both medical biobanks and forensic DNA databases, raises new questions that should be included in the ethical debate, in relation to both health services/medical research and activities associated with the criminal justice system. PMID:26139851

  4. About DNA databasing and investigative genetic analysis of externally visible characteristics: A public survey.

    PubMed

    Zieger, Martin; Utz, Silvia

    2015-07-01

    During the last decade, DNA profiling and the use of DNA databases have become two of the most employed instruments of police investigations. This very rapid establishment of forensic genetics is yet far from being complete. In the last few years novel types of analyses have been presented to describe phenotypically a possible perpetrator. We conducted the present study among German speaking Swiss residents for two main reasons: firstly, we aimed at getting an impression of the public awareness and acceptance of the Swiss DNA database and the perception of a hypothetical DNA database containing all Swiss residents. Secondly, we wanted to get a broader picture of how people that are not working in the field of forensic genetics think about legal permission to establish phenotypic descriptions of alleged criminals by genetic means. Even though a significant number of study participants did not even know about the existence of the Swiss DNA database, its acceptance appears to be very high. Generally our results suggest that the current forensic use of DNA profiling is considered highly trustworthy. However, the acceptance of a hypothetical universal database would be only as low as about 30% among the 284 respondents to our study, mostly because people are concerned about the security of their genetic data, their privacy or a possible risk of abuse of such a database. Concerning the genetic analysis of externally visible characteristics and biogeographical ancestry, we discover a high degree of acceptance. The acceptance decreases slightly when precise characteristics are presented to the participants in detail. About half of the respondents would be in favor of the moderate use of physical traits analyses only for serious crimes threatening life, health or sexual integrity. The possible risk of discrimination and reinforcement of racism, as discussed by scholars from anthropology, bioethics, law, philosophy and sociology, is mentioned less frequently by the study

  5. Spanish public awareness regarding DNA profile databases in forensic genetics: what type of DNA profiles should be included?

    PubMed Central

    Gamero, Joaquín J; Romero, Jose‐Luis; Peralta, Juan‐Luis; Carvalho, Mónica; Corte‐Real, Francisco

    2007-01-01

    The importance of non‐codifying DNA polymorphism for the administration of justice is now well known. In Spain, however, this type of test has given rise to questions in recent years: (a) Should consent be obtained before biological samples are taken from an individual for DNA analysis? (b) Does society perceive these techniques and methods of analysis as being reliable? (c) There appears to be lack of knowledge concerning the basic norms that regulate databases containing private or personal information and the protection that information of this type must be given. This opinion survey and the subsequent analysis of the results in ethical terms may serve to reveal the criteria and the degree of information that society has with regard to DNA databases. In the study, 73.20% (SE 1.12%) of the population surveyed was in favour of specific legislation for computer files in which DNA analysis results for forensic purposes are stored. PMID:17906059

  6. NCCDPHP PUBLICATION DATABASE

    EPA Science Inventory

    This database provides bibliographic citations and abstracts of publications produced by the CDC's National Center for Chronic Disease Prevention and Health Promotion (NCCDPHP) including journal articles, monographs, book chapters, reports, policy documents, and fact sheets. Full...

  7. Navigating Public Microarray Databases

    PubMed Central

    Bähler, Jürg

    2004-01-01

    With the ever-escalating amount of data being produced by genome-wide microarray studies, it is of increasing importance that these data are captured in public databases so that researchers can use this information to complement and enhance their own studies. Many groups have set up databases of expression data, ranging from large repositories, which are designed to comprehensively capture all published data, through to more specialized databases. The public repositories, such as ArrayExpress at the European Bioinformatics Institute contain complete datasets in raw format in addition to processed data, whilst the specialist databases tend to provide downstream analysis of normalized data from more focused studies and data sources. Here we provide a guide to the use of these public microarray resources. PMID:18629145

  8. Navigating public microarray databases.

    PubMed

    Penkett, Christopher J; Bähler, Jürg

    2004-01-01

    With the ever-escalating amount of data being produced by genome-wide microarray studies, it is of increasing importance that these data are captured in public databases so that researchers can use this information to complement and enhance their own studies. Many groups have set up databases of expression data, ranging from large repositories, which are designed to comprehensively capture all published data, through to more specialized databases. The public repositories, such as ArrayExpress at the European Bioinformatics Institute contain complete datasets in raw format in addition to processed data, whilst the specialist databases tend to provide downstream analysis of normalized data from more focused studies and data sources. Here we provide a guide to the use of these public microarray resources. PMID:18629145

  9. Enhancing the DNA Patent Database

    SciTech Connect

    Walters, LeRoy B.

    2008-02-18

    Final Report on Award No. DE-FG0201ER63171 Principal Investigator: LeRoy B. Walters February 18, 2008 This project successfully completed its goal of surveying and reporting on the DNA patenting and licensing policies at 30 major U.S. academic institutions. The report of survey results was published in the January 2006 issue of Nature Biotechnology under the title “The Licensing of DNA Patents by US Academic Institutions: An Empirical Survey.” Lori Pressman was the lead author on this feature article. A PDF reprint of the article will be submitted to our Program Officer under separate cover. The project team has continued to update the DNA Patent Database on a weekly basis since the conclusion of the project. The database can be accessed at dnapatents.georgetown.edu. This database provides a valuable research tool for academic researchers, policymakers, and citizens. A report entitled Reaping the Benefits of Genomic and Proteomic Research: Intellectual Property Rights, Innovation, and Public Health was published in 2006 by the Committee on Intellectual Property Rights in Genomic and Protein Research and Innovation, Board on Science, Technology, and Economic Policy at the National Academies. The report was edited by Stephen A. Merrill and Anne-Marie Mazza. This report employed and then adapted the methodology developed by our research project and quoted our findings at several points. (The full report can be viewed online at the following URL: http://www.nap.edu/openbook.php?record_id=11487&page=R1). My colleagues and I are grateful for the research support of the ELSI program at the U.S. Department of Energy.

  10. Developing a DNA variant database.

    PubMed

    Fung, David C Y

    2008-01-01

    Disease- and locus-specific variant databases have been a valuable resource to clinical and research geneticists. With the recent rapid developments in technologies, the number of DNA variants detected in a typical molecular genetics laboratory easily exceeds 1,000. To keep track of the growing inventory of DNA variants, many laboratories employ information technology to store the data as well as distributing the data and its associated information to clinicians and researchers via the Web. While it is a valuable resource, the hosting of a web-accessible database requires collaboration between bioinformaticians and biologists and careful planning to ensure its usability and availability. In this chapter, a series of tutorials on building a local DNA variant database out of a sample dataset will be provided. However, this tutorial will not include programming details on building a web interface and on constructing the web application necessary for web hosting. Instead, an introduction to the two commonly used methods for hosting web-accessible variant databases will be described. Apart from the tutorials, this chapter will also consider the resources and planning required for making a variant database project successful. PMID:18453092

  11. AIDS PUBLIC INFORMATION DATABASE

    EPA Science Inventory

    The AIDS Public Information Data Set is computer software designed to run on a Microsoft Windows microcomputer, and contains information abstracted from acquired immunodeficiency syndrome (AIDS) cases reported in the United States. The data set is created by the Division of HIV/A...

  12. Short Tandem Repeat DNA Internet Database

    National Institute of Standards and Technology Data Gateway

    SRD 130 Short Tandem Repeat DNA Internet Database (Web, free access)   Short Tandem Repeat DNA Internet Database is intended to benefit research and application of short tandem repeat DNA markers for human identity testing. Facts and sequence information on each STR system, population data, commonly used multiplex STR systems, PCR primers and conditions, and a review of various technologies for analysis of STR alleles have been included.

  13. Forensic DNA Profiling and Database

    PubMed Central

    Panneerchelvam, S.; Norazmi, M.N.

    2003-01-01

    The incredible power of DNA technology as an identification tool had brought a tremendous change in crimnal justice . DNA data base is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers. This article discusses the essential steps in compilation of COmbined DNA Index System (CODIS) on validated polymerase chain amplified STRs and their use in crime detection. PMID:23386793

  14. Database Support for Research in Public Administration

    ERIC Educational Resources Information Center

    Tucker, James Cory

    2005-01-01

    This study examines the extent to which databases support student and faculty research in the area of public administration. A list of journals in public administration, public policy, political science, public budgeting and finance, and other related areas was compared to the journal content list of six business databases. These databases…

  15. The Protein-DNA Interface database

    PubMed Central

    2010-01-01

    The Protein-DNA Interface database (PDIdb) is a repository containing relevant structural information of Protein-DNA complexes solved by X-ray crystallography and available at the Protein Data Bank. The database includes a simple functional classification of the protein-DNA complexes that consists of three hierarchical levels: Class, Type and Subtype. This classification has been defined and manually curated by humans based on the information gathered from several sources that include PDB, PubMed, CATH, SCOP and COPS. The current version of the database contains only structures with resolution of 2.5 Å or higher, accounting for a total of 922 entries. The major aim of this database is to contribute to the understanding of the main rules that underlie the molecular recognition process between DNA and proteins. To this end, the database is focused on each specific atomic interface rather than on the separated binding partners. Therefore, each entry in this database consists of a single and independent protein-DNA interface. We hope that PDIdb will be useful to many researchers working in fields such as the prediction of transcription factor binding sites in DNA, the study of specificity determinants that mediate enzyme recognition events, engineering and design of new DNA binding proteins with distinct binding specificity and affinity, among others. Finally, due to its friendly and easy-to-use web interface, we hope that PDIdb will also serve educational and teaching purposes. PMID:20482798

  16. DNA reviews: the national DNA database of the United Kingdom.

    PubMed

    Graham, E A M

    2007-12-01

    The national DNA database in United Kingdom has now been operational for over 10 years. This review looks at the history and development of this investigative resource. From the development of commercial DNA profiling kits to the current statistics for matches obtained in relation to criminal investigation in the United Kingdom, before moving onto discussing potential future direction that national DNA databases might take, including international collaboration on a European and global scale. PMID:25869270

  17. DNA Motif Databases and Their Uses.

    PubMed

    Stormo, Gary D

    2015-01-01

    Transcription factors (TFs) recognize and bind to specific DNA sequences. The specificity of a TF is usually represented as a position weight matrix (PWM). Several databases of DNA motifs exist and are used in biological research to address important biological questions. This overview describes PWMs and some of the most commonly used motif databases, as well as a few of their common applications. PMID:26334922

  18. Publications of Australian LIS Academics in Databases

    ERIC Educational Resources Information Center

    Wilson, Concepcion S.; Boell, Sebastian K.; Kennan, Mary Anne; Willard, Patricia

    2011-01-01

    This paper examines aspects of journal articles published from 1967 to 2008, located in eight databases, and authored or co-authored by academics serving for at least two years in Australian LIS programs from 1959 to 2008. These aspects are: inclusion of publications in databases, publications in journals, authorship characteristics of…

  19. Plant rDNA database: update and new features

    PubMed Central

    Garcia, Sònia; Gálvez, Francisco; Gras, Airy; Kovařík, Aleš; Garnatje, Teresa

    2014-01-01

    The Plant rDNA database (www.plantrdnadatabase.com) is an open access online resource providing detailed information on numbers, structures and positions of 5S and 18S-5.8S-26S (35S) ribosomal DNA loci. The data have been obtained from >600 publications on plant molecular cytogenetics, mostly based on fluorescent in situ hybridization (FISH). This edition of the database contains information on 1609 species derived from 2839 records, which means an expansion of 55.76 and 94.45%, respectively. It holds the data for angiosperms, gymnosperms, bryophytes and pteridophytes available as of June 2013. Information from publications reporting data for a single rDNA (either 5S or 35S alone) and annotation regarding transcriptional activity of 35S loci now appears in the database. Preliminary analyses suggest greater variability in the number of rDNA loci in gymnosperms than in angiosperms. New applications provide ideograms of the species showing the positions of rDNA loci as well as a visual representation of their genome sizes. We have also introduced other features to boost the usability of the Web interface, such as an application for convenient data export and a new section with rDNA–FISH-related information (mostly detailing protocols and reagents). In addition, we upgraded and/or proofread tabs and links and modified the website for a more dynamic appearance. This manuscript provides a synopsis of these changes and developments. Database URL: http://www.plantrdnadatabase.com PMID:24980131

  20. Influencing Database Use in Public Libraries.

    ERIC Educational Resources Information Center

    Tenopir, Carol

    1999-01-01

    Discusses results of a survey of factors influencing database use in public libraries. Highlights the importance of content; ease of use; and importance of instruction. Tabulates importance indications for number and location of workstations, library hours, availability of remote login, usefulness and quality of content, lack of other databases,…

  1. Public Opinion Poll Question Databases: An Evaluation

    ERIC Educational Resources Information Center

    Woods, Stephen

    2007-01-01

    This paper evaluates five polling resource: iPOLL, Polling the Nations, Gallup Brain, Public Opinion Poll Question Database, and Polls and Surveys. Content was evaluated on disclosure standards from major polling organizations, scope on a model for public opinion polls, and presentation on a flow chart discussing search limitations and usability.

  2. Ethical-legal problems of DNA databases in criminal investigation.

    PubMed

    Guillén, M; Lareu, M V; Pestoni, C; Salas, A; Carracedo, A

    2000-08-01

    Advances in DNA technology and the discovery of DNA polymorphisms have permitted the creation of DNA databases of individuals for the purpose of criminal investigation. Many ethical and legal problems arise in the preparation of a DNA database, and these problems are especially important when one analyses the legal regulations on the subject. In this paper three main groups of possibilities, three systems, are analysed in relation to databases. The first system is based on a general analysis of the population; the second one is based on the taking of samples for a particular list of crimes, and a third is based only on the specific analysis of each case. The advantages and disadvantages of each system are compared and controversial issues are then examined. We found the second system to be the best choice for Spain and other European countries with a similar tradition when we weighed the rights of an individual against the public's interest in the prosecution of a crime. PMID:10951922

  3. DDRprot: a database of DNA damage response-related proteins

    PubMed Central

    Andrés-León, Eduardo; Cases, Ildefonso; Arcas, Aida; Rojas, Ana M.

    2016-01-01

    The DNA Damage Response (DDR) signalling network is an essential system that protects the genome’s integrity. The DDRprot database presented here is a resource that integrates manually curated information on the human DDR network and its sub-pathways. For each particular DDR protein, we present detailed information about its function. If involved in post-translational modifications (PTMs) with each other, we depict the position of the modified residue/s in the three-dimensional structures, when resolved structures are available for the proteins. All this information is linked to the original publication from where it was obtained. Phylogenetic information is also shown, including time of emergence and conservation across 47 selected species, family trees and sequence alignments of homologues. The DDRprot database can be queried by different criteria: pathways, species, evolutionary age or involvement in (PTM). Sequence searches using hidden Markov models can be also used. Database URL: http://ddr.cbbio.es. PMID:27577567

  4. DDRprot: a database of DNA damage response-related proteins.

    PubMed

    Andrés-León, Eduardo; Cases, Ildefonso; Arcas, Aida; Rojas, Ana M

    2016-01-01

    The DNA Damage Response (DDR) signalling network is an essential system that protects the genome's integrity. The DDRprot database presented here is a resource that integrates manually curated information on the human DDR network and its sub-pathways. For each particular DDR protein, we present detailed information about its function. If involved in post-translational modifications (PTMs) with each other, we depict the position of the modified residue/s in the three-dimensional structures, when resolved structures are available for the proteins. All this information is linked to the original publication from where it was obtained. Phylogenetic information is also shown, including time of emergence and conservation across 47 selected species, family trees and sequence alignments of homologues. The DDRprot database can be queried by different criteria: pathways, species, evolutionary age or involvement in (PTM). Sequence searches using hidden Markov models can be also used.Database URL: http://ddr.cbbio.es. PMID:27577567

  5. The Dfam database of repetitive DNA families

    PubMed Central

    Hubley, Robert; Finn, Robert D.; Clements, Jody; Eddy, Sean R.; Jones, Thomas A.; Bao, Weidong; Smit, Arian F.A.; Wheeler, Travis J.

    2016-01-01

    Repetitive DNA, especially that due to transposable elements (TEs), makes up a large fraction of many genomes. Dfam is an open access database of families of repetitive DNA elements, in which each family is represented by a multiple sequence alignment and a profile hidden Markov model (HMM). The initial release of Dfam, featured in the 2013 NAR Database Issue, contained 1143 families of repetitive elements found in humans, and was used to produce more than 100 Mb of additional annotation of TE-derived regions in the human genome, with improved speed. Here, we describe recent advances, most notably expansion to 4150 total families including a comprehensive set of known repeat families from four new organisms (mouse, zebrafish, fly and nematode). We describe improvements to coverage, and to our methods for identifying and reducing false annotation. We also describe updates to the website interface. The Dfam website has moved to http://dfam.org. Seed alignments, profile HMMs, hit lists and other underlying data are available for download. PMID:26612867

  6. The Dfam database of repetitive DNA families.

    PubMed

    Hubley, Robert; Finn, Robert D; Clements, Jody; Eddy, Sean R; Jones, Thomas A; Bao, Weidong; Smit, Arian F A; Wheeler, Travis J

    2016-01-01

    Repetitive DNA, especially that due to transposable elements (TEs), makes up a large fraction of many genomes. Dfam is an open access database of families of repetitive DNA elements, in which each family is represented by a multiple sequence alignment and a profile hidden Markov model (HMM). The initial release of Dfam, featured in the 2013 NAR Database Issue, contained 1143 families of repetitive elements found in humans, and was used to produce more than 100 Mb of additional annotation of TE-derived regions in the human genome, with improved speed. Here, we describe recent advances, most notably expansion to 4150 total families including a comprehensive set of known repeat families from four new organisms (mouse, zebrafish, fly and nematode). We describe improvements to coverage, and to our methods for identifying and reducing false annotation. We also describe updates to the website interface. The Dfam website has moved to http://dfam.org. Seed alignments, profile HMMs, hit lists and other underlying data are available for download. PMID:26612867

  7. A compendium of human mitochondrial DNA control region: development of an international standard forensic database.

    PubMed

    Miller, K W; Budowle, B

    2001-06-01

    A compendium of human mitochondrial DNA (mtDNA) control region types has been constructed. This updated compilation indexes over 10,000 population-specific mtDNA nucleotide sequences in a standardized format. The sequences represent mtDNA types from the Scientific Working Group on DNA Analysis Methods (SWGDAM) mtDNA database and from the public literature. The SWGDAM data are considered to be of higher quality than the public data, particularly for counting the number of times a particular haplotype has been observed. PMID:11387646

  8. 24 CFR 81.72 - Public-use database and public information.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 1 2010-04-01 2010-04-01 false Public-use database and public... Public-use database and public information. (a) General. Except as provided in paragraph (c) of this section, the Secretary shall establish and make available for public use, a public-use database...

  9. 24 CFR 81.72 - Public-use database and public information.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 24 Housing and Urban Development 1 2013-04-01 2013-04-01 false Public-use database and public... Public-use database and public information. (a) General. Except as provided in paragraph (c) of this section, the Secretary shall establish and make available for public use, a public-use database...

  10. 24 CFR 81.72 - Public-use database and public information.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 24 Housing and Urban Development 1 2011-04-01 2011-04-01 false Public-use database and public... Public-use database and public information. (a) General. Except as provided in paragraph (c) of this section, the Secretary shall establish and make available for public use, a public-use database...

  11. 24 CFR 81.72 - Public-use database and public information.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 24 Housing and Urban Development 1 2014-04-01 2014-04-01 false Public-use database and public... Public-use database and public information. (a) General. Except as provided in paragraph (c) of this section, the Secretary shall establish and make available for public use, a public-use database...

  12. 24 CFR 81.72 - Public-use database and public information.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 24 Housing and Urban Development 1 2012-04-01 2012-04-01 false Public-use database and public... Public-use database and public information. (a) General. Except as provided in paragraph (c) of this section, the Secretary shall establish and make available for public use, a public-use database...

  13. The Availability of Faculty Publication Databases from Library Web Pages

    ERIC Educational Resources Information Center

    Blummer, Barbara A.

    2007-01-01

    Faculty publication databases or author bibliographies offer libraries an opportunity to provide services to users. Initially, these databases remained initiatives of special libraries in the health-sciences fields. Librarians used the publication information derived from these databases to compile lists for annual reports. However, the advent of…

  14. Exploration of the Chemical Space of Public Genomic Databases

    EPA Science Inventory

    The current project aims to chemically index the content of public genomic databases to make these data accessible in relation to other publicly available, chemically-indexed toxicological information.

  15. 75 FR 29155 - Publicly Available Consumer Product Safety Information Database

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-24

    ...The Consumer Product Safety Commission (``Commission,'' ``CPSC,'' or ``we'') is issuing a notice of proposed rulemaking that would establish a publicly available consumer product safety information database (``database''). Section 212 of the Consumer Product Safety Improvement Act of 2008 (``CPSIA'') amended the Consumer Product Safety Act (``CPSA'') to require the Commission to establish and......

  16. The Israel DNA database--the establishment of a rapid, semi-automated analysis system.

    PubMed

    Zamir, Ashira; Dell'Ariccia-Carmon, Aviva; Zaken, Neomi; Oz, Carla

    2012-03-01

    The Israel Police DNA database, also known as IPDIS (Israel Police DNA Index System), has been operating since February 2007. During that time more than 135,000 reference samples have been uploaded and more than 2000 hits reported. We have developed an effective semi-automated system that includes two automated punchers, three liquid handler robots and four genetic analyzers. An inhouse LIMS program enables full tracking of every sample through the entire process of registration, pre-PCR handling, analysis of profiles, uploading to the database, hit reports and ultimately storage. The LIMS is also responsible for the future tracking of samples and their profiles to be expunged from the database according to the Israeli DNA legislation. The database is administered by an in-house developed software program, where reference and evidentiary profiles are uploaded, stored, searched and matched. The DNA database has proven to be an effective investigative tool which has gained the confidence of the Israeli public and on which the Israel National Police force has grown to rely. PMID:21727053

  17. The Human Variome Project: ensuring the quality of DNA variant databases in inherited renal disease.

    PubMed

    Savige, Judy; Dalgleish, Raymond; Cotton, Richard Gh; den Dunnen, Johan T; Macrae, Finlay; Povey, Sue

    2015-11-01

    A recent review identified 60 common inherited renal diseases caused by DNA variants in 132 different genes. These diseases can be diagnosed with DNA sequencing, but each gene probably also has a thousand normal variants. Many more normal variants have been characterised by individual laboratories than are reported in the literature or found in publicly accessible collections. At present, testing laboratories must assess each novel change they identify for pathogenicity, even when this has been done elsewhere previously, and the distinction between normal and disease-associated variants is particularly an issue with the recent surge in exomic sequencing and gene discovery projects. The Human Variome Project recommends the establishment of gene-specific DNA variant databases to facilitate the sharing of DNA variants and decisions about likely disease causation. Databases improve diagnostic accuracy and testing efficiency, and reduce costs. They also help with genotype-phenotype correlations and predictive algorithms. The Human Variome Project advocates databases that use standardised descriptions, are up-to-date, include clinical information and are freely available. Currently, the genes affected in the most common inherited renal diseases correspond to 350 different variant databases, many of which are incomplete or have insufficient clinical details for genotype-phenotype correlations. Assistance is needed from nephrologists to maximise the usefulness of these databases for the diagnosis and management of inherited renal disease. PMID:25384529

  18. Choice of population database for forensic DNA profile analysis.

    PubMed

    Steele, Christopher D; Balding, David J

    2014-12-01

    When evaluating the weight of evidence (WoE) for an individual to be a contributor to a DNA sample, an allele frequency database is required. The allele frequencies are needed to inform about genotype probabilities for unknown contributors of DNA to the sample. Typically databases are available from several populations, and a common practice is to evaluate the WoE using each available database for each unknown contributor. Often the most conservative WoE (most favourable to the defence) is the one reported to the court. However the number of human populations that could be considered is essentially unlimited and the number of contributors to a sample can be large, making it impractical to perform every possible WoE calculation, particularly for complex crime scene profiles. We propose instead the use of only the database that best matches the ancestry of the queried contributor, together with a substantial FST adjustment. To investigate the degree of conservativeness of this approach, we performed extensive simulations of one- and two-contributor crime scene profiles, in the latter case with, and without, the profile of the second contributor available for the analysis. The genotypes were simulated using five population databases, which were also available for the analysis, and evaluations of WoE using our heuristic rule were compared with several alternative calculations using different databases. Using FST=0.03, we found that our heuristic gave WoE more favourable to the defence than alternative calculations in well over 99% of the comparisons we considered; on average the difference in WoE was just under 0.2 bans (orders of magnitude) per locus. The degree of conservativeness of the heuristic rule can be adjusted through the FST value. We propose the use of this heuristic for DNA profile WoE calculations, due to its ease of implementation, and efficient use of the evidence while allowing a flexible degree of conservativeness. PMID:25498938

  19. DNAVaxDB: the first web-based DNA vaccine database and its data analysis.

    PubMed

    Racz, Rebecca; Li, Xinna; Patel, Mukti; Xiang, Zuoshuang; He, Yongqun

    2014-01-01

    Since the first DNA vaccine studies were done in the 1990s, thousands more studies have followed. Here we report the development and analysis of DNAVaxDB (http://www.violinet.org/dnavaxdb), the first publically available web-based DNA vaccine database that curates, stores, and analyzes experimentally verified DNA vaccines, DNA vaccine plasmid vectors, and protective antigens used in DNA vaccines. All data in DNAVaxDB are annotated from reliable resources, particularly peer-reviewed articles. Among over 140 DNA vaccine plasmids, some plasmids were more frequently used in one type of pathogen than others; for example, pCMVi-UB for G- bacterial DNA vaccines, and pCAGGS for viral DNA vaccines. Presently, over 400 DNA vaccines containing over 370 protective antigens from over 90 infectious and non-infectious diseases have been curated in DNAVaxDB. While extracellular and bacterial cell surface proteins and adhesin proteins were frequently used for DNA vaccine development, the majority of protective antigens used in Chlamydophila DNA vaccines are localized to the inner portion of the cell. The DNA vaccine priming, other vaccine boosting vaccination regimen has been widely used to induce protection against infection of different pathogens such as HIV. Parasitic and cancer DNA vaccines were also systematically analyzed. User-friendly web query and visualization interfaces are available in DNAVaxDB for interactive data search. To support data exchange, the information of DNA vaccines, plasmids, and protective antigens is stored in the Vaccine Ontology (VO). DNAVaxDB is targeted to become a timely and vital source of DNA vaccines and related data and facilitate advanced DNA vaccine research and development. PMID:25104313

  20. DNAVaxDB: the first web-based DNA vaccine database and its data analysis

    PubMed Central

    2014-01-01

    Since the first DNA vaccine studies were done in the 1990s, thousands more studies have followed. Here we report the development and analysis of DNAVaxDB (http://www.violinet.org/dnavaxdb), the first publically available web-based DNA vaccine database that curates, stores, and analyzes experimentally verified DNA vaccines, DNA vaccine plasmid vectors, and protective antigens used in DNA vaccines. All data in DNAVaxDB are annotated from reliable resources, particularly peer-reviewed articles. Among over 140 DNA vaccine plasmids, some plasmids were more frequently used in one type of pathogen than others; for example, pCMVi-UB for G- bacterial DNA vaccines, and pCAGGS for viral DNA vaccines. Presently, over 400 DNA vaccines containing over 370 protective antigens from over 90 infectious and non-infectious diseases have been curated in DNAVaxDB. While extracellular and bacterial cell surface proteins and adhesin proteins were frequently used for DNA vaccine development, the majority of protective antigens used in Chlamydophila DNA vaccines are localized to the inner portion of the cell. The DNA vaccine priming, other vaccine boosting vaccination regimen has been widely used to induce protection against infection of different pathogens such as HIV. Parasitic and cancer DNA vaccines were also systematically analyzed. User-friendly web query and visualization interfaces are available in DNAVaxDB for interactive data search. To support data exchange, the information of DNA vaccines, plasmids, and protective antigens is stored in the Vaccine Ontology (VO). DNAVaxDB is targeted to become a timely and vital source of DNA vaccines and related data and facilitate advanced DNA vaccine research and development. PMID:25104313

  1. Enhancing thermal video using a public database of images

    NASA Astrophysics Data System (ADS)

    Qadir, Hemin; Kozaitis, S. P.; Ali, Ehsan

    2014-05-01

    We presented a system to display nightime imagery with natural colors using a public database of images. We initially combined two spectral bands of images, thermal and visible, to enhance night vision imagery, however the fused image gave an unnatural color appearance. Therefore, a color transfer based on look-up table (LUT) was used to replace the false color appearance with a colormap derived from a daytime reference image obtained from a public database using the GPS coordinates of the vehicle. Because of the computational demand in deriving the colormap from the reference image, we created an additional local database of colormaps. Reference images from the public database were compared to a compact local database to retrieve one of a limited number of colormaps that represented several driving environments. Each colormap in the local database was stored with an image from which it was derived. To retrieve a colormap, we compared the histogram of the fused image with histograms of images in the local database. The colormaps of the best match was then used for the fused image. Continuously selecting and applying colormaps using this approach offered a convenient way to color night vision imagery.

  2. Building a Faculty Publications Database: A Case Study

    ERIC Educational Resources Information Center

    Tabaei, Sara; Schaffer, Yitzchak; McMurray, Gregory; Simon, Bashe

    2013-01-01

    This case study shares the experience of building an in-house faculty publications database that was spearheaded by the Touro College and University System library in 2010. The project began with the intention of contributing to the college by collecting the research accomplishments of our faculty and staff, thereby also increasing library…

  3. Digital Equipment Corporation's CRDOM Software and Database Publications.

    ERIC Educational Resources Information Center

    Adams, Michael Q.

    1986-01-01

    Acquaints information professionals with Digital Equipment Corporation's compact optical disk read-only-memory (CDROM) search and retrieval software and growing library of CDROM database publications (COMPENDEX, Chemical Abstracts Services). Highlights include MicroBASIS, boolean operators, range operators, word and phrase searching, proximity…

  4. A study of Spanish attitudes regarding the custody and use of forensic DNA databases.

    PubMed

    Gamero, Joaquín-Jose; Romero, José-Luis; Peralta, Juan-Luis; Corte-Real, Francisco; Guillén, Margarita; Anjos, Maria-Joao

    2008-03-01

    One of the issues that has resulted in much disagreement in many countries at different levels concerns the kind of institution that should be given the responsibility of exercising custody over biological samples and the DNA profiles obtained from these samples. In the field of forensic genetics, there is no doubt that the existence of DNA criminal databases benefits the control and investigation of crime. However, certain criticism, supported to a great extent by the particular vision of genetic exceptionalism has been aimed at the ethical and social consequences resulting from the inappropriate use of such databases. In this sense, it was stated that the support of the population was required for those regulations that propose the extension of police powers in the collection and storage of biological samples, as well as their corresponding DNA analyses. Without such backing, such measures may cause society to distrust the nature of the protection afforded by the legal system and be interpreted as interference in the civil liberties and human rights of the individual. We believe that the opinion poll which has been carried out among the Spanish population may serve to reveal the public attitudes/criteria which society has with regard to those institutions responsible for the custody of DNA profile databases. Finally, it must be pointed out that when the interviewees were asked about what institution or institutions should protect and maintain data confidentiality 59.7% considered that custody should remain in the hands of the National Agency for DNA Profiles (a judicially backed, autonomous public institution). PMID:19083809

  5. Genetics and Forensics: Making the National DNA Database

    PubMed Central

    Johnson, Paul; Williams, Robin; Martin, Paul

    2005-01-01

    This paper is based on a current study of the growing police use of the epistemic authority of molecular biology for the identification of criminal suspects in support of crime investigation. It discusses the development of DNA profiling and the establishment and development of the UK National DNA Database (NDNAD) as an instance of the ‘scientification of police work’ (Ericson and Shearing 1986) in which the police uses of science and technology have a recursive effect on their future development. The NDNAD, owned by the Association of Chief Police Officers of England and Wales, is the first of its kind in the world and currently contains the genetic profiles of more than 2 million people. The paper provides a framework for the examination of this socio-technical innovation, begins to tease out the dense and compact history of the database and accounts for the way in which changes and developments across disparate scientific, governmental and policing contexts, have all contributed to the range of uses to which it is put. PMID:16467921

  6. A publication database for optical long baseline interferometry

    NASA Astrophysics Data System (ADS)

    Malbet, Fabien; Mella, Guillaume; Lawson, Peter; Taillifet, Esther; Lafrasse, Sylvain

    2010-07-01

    Optical long baseline interferometry is a technique that has generated almost 850 refereed papers to date. The targets span a large variety of objects from planetary systems to extragalactic studies and all branches of stellar physics. We have created a database hosted by the JMMC and connected to the Optical Long Baseline Interferometry Newsletter (OLBIN) web site using MySQL and a collection of XML or PHP scripts in order to store and classify these publications. Each entry is defined by its ADS bibcode, includes basic ADS informations and metadata. The metadata are specified by tags sorted in categories: interferometric facilities, instrumentation, wavelength of operation, spectral resolution, type of measurement, target type, and paper category, for example. The whole OLBIN publication list has been processed and we present how the database is organized and can be accessed. We use this tool to generate statistical plots of interest for the community in optical long baseline interferometry.

  7. 76 FR 1137 - Publicly Available Consumer Product Safety Information Database: Notice of Public Web Conferences

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-07

    ... site. In the Federal Register of December 9, 2010 (75 FR 76832), we published a final rule to establish... COMMISSION Publicly Available Consumer Product Safety Information Database: Notice of Public Web Conferences... Commission (``Commission,'' ``CPSC,'' or ``we'') is announcing two Web conferences to demonstrate...

  8. Addressing the use of phylogenetics for identification of sequences in error in the SWGDAM mitochondrial DNA database.

    PubMed

    Budowle, Bruce; Polanskey, Deborah; Allard, Marc W; Chakraborty, Ranajit

    2004-11-01

    The SWGDAM mtDNA database is a publicly available reference source that is used for estimating the rarity of an evidence mtDNA profile. Because of the current processes for generating population data, it is unlikely that population databases are error free. The majority of the errors are due to human error and are transcriptional in nature. Phylogenetic analysis of data sets can identify some potential errors, and coupled with a review of the sequence data or alignment sheets can be a very useful tool. Seven sequences with errors have been identified by phylogenetic analysis. In addition, two samples were inadvertently modified when placed in the SWGDAM database. The corrected sequences are provided so that users can modify appropriately the current iteration of the SWGDAM database. From a practical perspective, upper bound estimates of the percentage of matching profiles obtained from a database search containing an incorrect sequence and those of a database containing the corrected sequence are not substantially different. Community wide access and review has enabled identification of errors in the SWGDAM data set and will continue to do so. The result of public accessibility is that the quality of the SWGDAM forensic dataset is always improving. PMID:15568698

  9. Tracking the violent criminal offender through DNA typing profiles--a national database system concept.

    PubMed

    Baechtel, F S; Monson, K L; Forsen, G E; Budowle, B; Kearney, J J

    1991-01-01

    Implementation of standard methods for the conduct of restriction fragment length polymorphism analysis into the protocols of United States crime laboratories offers an unprecedented opportunity for the establishment of a national computer database system to enable interchange of DNA typing information. The FBI Laboratory, in concert with crime laboratory representatives, has taken the initiative in planning and implementing such a database system. The Combined DNA Index System (CODIS) will be composed of three sub-indices: a statistical database, which will contain frequencies of DNA fragment alleles in various population groups; an investigative database which will enable linkage of violent crimes through a common subject; and a convicted felon database that will serve to maintain DNA typing profiles for comparison to profiles developed from violent crimes where the suspect may be unknown. PMID:1678357

  10. Exploring public databases to characterize urban flood risks in Amsterdam

    NASA Astrophysics Data System (ADS)

    Gaitan, Santiago; ten Veldhuis, Marie-claire; van de Giesen, Nick

    2015-04-01

    Cities worldwide are challenged by increasing urban flood risks. Precise and realistic measures are required to decide upon investment to reduce their impacts. Obvious flooding factors affecting flood risk include sewer systems performance and urban topography. However, currently implemented sewer and topographic models do not provide realistic predictions of local flooding occurrence during heavy rain events. Assessing other factors such as spatially distributed rainfall and socioeconomic characteristics may help to explain probability and impacts of urban flooding. Several public databases were analyzed: complaints about flooding made by citizens, rainfall depths (15 min and 100 Ha spatio-temporal resolution), grids describing number of inhabitants, income, and housing price (1Ha and 25Ha resolution); and buildings age. Data analysis was done using Python and GIS programming, and included spatial indexing of data, cluster analysis, and multivariate regression on the complaints. Complaints were used as a proxy to characterize flooding impacts. The cluster analysis, run for all the variables except the complaints, grouped part of the grid-cells of central Amsterdam into a highly differentiated group, covering 10% of the analyzed area, and accounting for 25% of registered complaints. The configuration of the analyzed variables in central Amsterdam coincides with a high complaint count. Remaining complaints were evenly dispersed along other groups. An adjusted R2 of 0.38 in the multivariate regression suggests that explaining power can improve if additional variables are considered. While rainfall intensity explained 4% of the incidence of complaints, population density and building age significantly explained around 20% each. Data mining of public databases proved to be a valuable tool to identify factors explaining variability in occurrence of urban pluvial flooding, though additional variables must be considered to fully explain flood risk variability.

  11. Forensic DNA databases in Western Balkan region: retrospectives, perspectives, and initiatives

    PubMed Central

    Marjanović, Damir; Konjhodžić, Rijad; Butorac, Sara Sanela; Drobnič, Katja; Merkaš, Siniša; Lauc, Gordan; Primorac, Damir; Anđelinović, Šimun; Milosavljević, Mladen; Karan, Željko; Vidović, Stojko; Stojković, Oliver; Panić, Bojana; Vučetić Dragović, Anđelka; Kovačević, Sandra; Jakovski, Zlatko; Asplen, Chris; Primorac, Dragan

    2011-01-01

    The European Network of Forensic Science Institutes (ENFSI) recommended the establishment of forensic DNA databases and specific implementation and management legislations for all EU/ENFSI members. Therefore, forensic institutions from Bosnia and Herzegovina, Serbia, Montenegro, and Macedonia launched a wide set of activities to support these recommendations. To assess the current state, a regional expert team completed detailed screening and investigation of the existing forensic DNA data repositories and associated legislation in these countries. The scope also included relevant concurrent projects and a wide spectrum of different activities in relation to forensics DNA use. The state of forensic DNA analysis was also determined in the neighboring Slovenia and Croatia, which already have functional national DNA databases. There is a need for a ‘regional supplement’ to the current documentation and standards pertaining to forensic application of DNA databases, which should include regional-specific preliminary aims and recommendations. PMID:21674821

  12. MitBASE : a comprehensive and integrated mitochondrial DNA database. The present status

    PubMed Central

    Attimonelli, M.; Altamura, N.; Benne, R.; Brennicke, A.; Cooper, J. M.; D’Elia, D.; Montalvo, A. de; Pinto, B. de; De Robertis, M.; Golik, P.; Knoop, V.; Lanave, C.; Lazowska, J.; Licciulli, F.; Malladi, B. S.; Memeo, F.; Monnerot, M.; Pasimeni, R.; Pilbout, S.; Schapira, A. H. V.; Sloof, P.; Saccone, C.

    2000-01-01

    MitBASE is an integrated and comprehensive database of mitochondrial DNA data which collects, under a single interface, databases for Plant, Vertebrate, Invertebrate, Human, Protist and Fungal mtDNA and a Pilot database on nuclear genes involved in mitochondrial biogenesis in Saccharomyces cerevisiae. MitBASE reports all available information from different organisms and from intraspecies variants and mutants. Data have been drawn from the primary databases and from the literature; value adding information has been structured, e.g., editing information on protist mtDNA genomes, pathological information for human mtDNA variants, etc. The different databases, some of which are structured using commercial packages (Microsoft Access, File Maker Pro) while others use a flat-file format, have been integrated under ORACLE. Ad hoc retrieval systems have been devised for some of the above listed databases keeping into account their peculiarities. The database is resident at the EBI and is available at the following site: http://www3.ebi.ac.uk/Research/Mitbase/mitbase.pl . The impact of this project is intended for both basic and applied research. The study of mitochondrial genetic diseases and mitochondrial DNA intraspecies diversity are key topics in several biotechnological fields. The database has been funded within the EU Biotechnology programme. PMID:10592207

  13. The EpiSLI Database: A Publicly Available Database on Speech and Language

    ERIC Educational Resources Information Center

    Tomblin, J. Bruce

    2010-01-01

    Purpose: This article describes a database that was created in the process of conducting a large-scale epidemiologic study of specific language impairment (SLI). As such, this database will be referred to as the EpiSLI database. Children with SLI have unexpected and unexplained difficulties learning and using spoken language. Although there is no…

  14. DNA Fingerprint Database for Crapemyrtle Cultivar Identification, Hybrid Verification, and Parentage Analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to create DNA fingerprints for the Razzle Dazzle® crape myrtle series using simple sequence repeat (SSR) markers, and compare them with the DNA fingerprints of a database made up of over 50 popular crape myrtle cultivars currently available in the trade. Data consiste...

  15. The Moroccan Genetic Disease Database (MGDD): a database for DNA variations related to inherited disorders and disease susceptibility.

    PubMed

    Charoute, Hicham; Nahili, Halima; Abidi, Omar; Gabi, Khalid; Rouba, Hassan; Fakiri, Malika; Barakat, Abdelhamid

    2014-03-01

    National and ethnic mutation databases provide comprehensive information about genetic variations reported in a population or an ethnic group. In this paper, we present the Moroccan Genetic Disease Database (MGDD), a catalogue of genetic data related to diseases identified in the Moroccan population. We used the PubMed, Web of Science and Google Scholar databases to identify available articles published until April 2013. The Database is designed and implemented on a three-tier model using Mysql relational database and the PHP programming language. To date, the database contains 425 mutations and 208 polymorphisms found in 301 genes and 259 diseases. Most Mendelian diseases in the Moroccan population follow autosomal recessive mode of inheritance (74.17%) and affect endocrine, nutritional and metabolic physiology. The MGDD database provides reference information for researchers, clinicians and health professionals through a user-friendly Web interface. Its content should be useful to improve researches in human molecular genetics, disease diagnoses and design of association studies. MGDD can be publicly accessed at http://mgdd.pasteur.ma. PMID:23860041

  16. Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase

    PubMed Central

    2009-01-01

    Background Although bivalves are among the most-studied marine organisms because of their ecological role and economic importance, very little information is available on the genome sequences of oyster species. This report documents three large-scale cDNA sequencing projects for the Pacific oyster Crassostrea gigas initiated to provide a large number of expressed sequence tags that were subsequently compiled in a publicly accessible database. This resource allowed for the identification of a large number of transcripts and provides valuable information for ongoing investigations of tissue-specific and stimulus-dependant gene expression patterns. These data are crucial for constructing comprehensive DNA microarrays, identifying single nucleotide polymorphisms and microsatellites in coding regions, and for identifying genes when the entire genome sequence of C. gigas becomes available. Description In the present paper, we report the production of 40,845 high-quality ESTs that identify 29,745 unique transcribed sequences consisting of 7,940 contigs and 21,805 singletons. All of these new sequences, together with existing public sequence data, have been compiled into a publicly-available Website http://public-contigbrowser.sigenae.org:9090/Crassostrea_gigas/index.html. Approximately 43% of the unique ESTs had significant matches against the SwissProt database and 27% were annotated using Gene Ontology terms. In addition, we identified a total of 208 in silico microsatellites from the ESTs, with 173 having sufficient flanking sequence for primer design. We also identified a total of 7,530 putative in silico, single-nucleotide polymorphisms using existing and newly-generated EST resources for the Pacific oyster. Conclusion A publicly-available database has been populated with 29,745 unique sequences for the Pacific oyster Crassostrea gigas. The database provides many tools to search cleaned and assembled ESTs. The user may input and submit several filters, such as

  17. DNA patenting: implications for public health research.

    PubMed Central

    Dutfield, Graham

    2006-01-01

    I weigh the arguments for and against the patenting of functional DNA sequences including genes, and find the objections to be compelling. Is an outright ban on DNA patenting the right policy response? Not necessarily. Governments may wish to consider options ranging from patent law reforms to the creation of new rights. There are alternative ways to protect DNA sequences that industry may choose if DNA patenting is restricted or banned. Some of these alternatives may be more harmful than patents. Such unintended consequences of patent bans mean that we should think hard before concluding that prohibition is the only response to legitimate concerns about the appropriateness of patents in the field of human genomics. PMID:16710549

  18. Database Changes (Post-Publication). ERIC Processing Manual, Section X.

    ERIC Educational Resources Information Center

    Brandhorst, Ted, Ed.

    The purpose of this section is to specify the procedure for making changes to the ERIC database after the data involved have been announced in the abstract journals RIE or CIJE. As a matter of general ERIC policy, a document or journal article is not re-announced or re-entered into the database as a new accession for the purpose of accomplishing a…

  19. Characterization and compilation of polymorphic simple sequence repeat (SSR) markers of peanut from public database

    PubMed Central

    2012-01-01

    Background There are several reports describing thousands of SSR markers in the peanut (Arachis hypogaea L.) genome. There is a need to integrate various research reports of peanut DNA polymorphism into a single platform. Further, because of lack of uniformity in the labeling of these markers across the publications, there is some confusion on the identities of many markers. We describe below an effort to develop a central comprehensive database of polymorphic SSR markers in peanut. Findings We compiled 1,343 SSR markers as detecting polymorphism (14.5%) within a total of 9,274 markers. Amongst all polymorphic SSRs examined, we found that AG motif (36.5%) was the most abundant followed by AAG (12.1%), AAT (10.9%), and AT (10.3%).The mean length of SSR repeats in dinucleotide SSRs was significantly longer than that in trinucleotide SSRs. Dinucleotide SSRs showed higher polymorphism frequency for genomic SSRs when compared to trinucleotide SSRs, while for EST-SSRs, the frequency of polymorphic SSRs was higher in trinucleotide SSRs than in dinucleotide SSRs. The correlation of the length of SSR and the frequency of polymorphism revealed that the frequency of polymorphism was decreased as motif repeat number increased. Conclusions The assembled polymorphic SSRs would enhance the density of the existing genetic maps of peanut, which could also be a useful source of DNA markers suitable for high-throughput QTL mapping and marker-assisted selection in peanut improvement and thus would be of value to breeders. PMID:22818284

  20. 75 FR 76831 - Publicly Available Consumer Product Safety Information Database

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-09

    ... available database. On May 24, 2010, we published a notice of proposed rulemaking at 75 FR 29156, which set... stakeholder input and comment, all of which were discussed in the preamble to the proposed rule at 75 FR 29156... (75 FR 29156, May 24, 2010) pertaining to each section. In addition to comments on each of...

  1. DOE's Public Database for Green Building Case Studies: Preprint

    SciTech Connect

    Torcellini, P. A.; Crawley, D. B.

    2003-11-01

    To help capture valuable information on''green building'' case studies, the U.S. Department of Energy has created an online database for collecting, standardizing, and disseminating information about high-performance, green projects. Type of information collected includes green features, design processes, energy performance, and comparison to other high-performance, green buildings.

  2. From Relationships to Relationship Marketing: Applying Database Technology to Public Relations.

    ERIC Educational Resources Information Center

    Petrison, Lisa A.; Wang, Paul

    1993-01-01

    Notes that advances in new technologies and uses of databases have expanded the definition of publics and increased the ability to target messages to narrower and narrower ranges of publics. Explores the implications of these developments for the public relations profession. (RS)

  3. Characterizing the genetic structure of a forensic DNA database using a latent variable approach.

    PubMed

    Kruijver, Maarten

    2016-07-01

    Several problems in forensic genetics require a representative model of a forensic DNA database. Obtaining an accurate representation of the offender database can be difficult, since databases typically contain groups of persons with unregistered ethnic origins in unknown proportions. We propose to estimate the allele frequencies of the subpopulations comprising the offender database and their proportions from the database itself using a latent variable approach. We present a model for which parameters can be estimated using the expectation maximization (EM) algorithm. This approach does not rely on relatively small and possibly unrepresentative population surveys, but is driven by the actual genetic composition of the database only. We fit the model to a snapshot of the Dutch offender database (2014), which contains close to 180,000 profiles, and find that three subpopulations suffice to describe a large fraction of the heterogeneity in the database. We demonstrate the utility and reliability of the approach with three applications. First, we use the model to predict the number of false leads obtained in database searches. We assess how well the model predicts the number of false leads obtained in mock searches in the Dutch offender database, both for the case of familial searching for first degree relatives of a donor and searching for contributors to three-person mixtures. Second, we study the degree of partial matching between all pairs of profiles in the Dutch database and compare this to what is predicted using the latent variable approach. Third, we use the model to provide evidence to support that the Dutch practice of estimating match probabilities using the Balding-Nichols formula with a native Dutch reference database and θ=0.03 is conservative. PMID:27128695

  4. An Internet-Accessible DNA Sequence Database for Identifying Fusaria from Human and Animal Infections

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Because less than one-third of clinically relevant fusaria can be accurately identified to species level using phenotypic data (i.e., morphological species recognition), we constructed a three-locus DNA sequence database to facilitate molecular identification of the 69 Fusarium species associated wi...

  5. DSSTOX WEBSITE LAUNCH: IMPROVING PUBLIC ACCESS TO DATABASES FOR BUILDING STRUCTURE-TOXICITY PREDICTION MODELS

    EPA Science Inventory

    DSSTox Website Launch: Improving Public Access to Databases for Building Structure-Toxicity Prediction Models
    Ann M. Richard
    US Environmental Protection Agency, Research Triangle Park, NC, USA

    Distributed: Decentralized set of standardized, field-delimited databases,...

  6. 75 FR 41180 - Notice of Order: Revisions to Enterprise Public Use Database

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-15

    ... matrices as set forth in HUD's October 4, 2004 Final Order. See 69 FR 59476. The PUDB matrices are data... AGENCY Notice of Order: Revisions to Enterprise Public Use Database AGENCY: Federal Housing Finance... use database (PUDB) for such mortgage data was transferred to FHFA from the U.S. Department of...

  7. End-Users/Public Access. Reprints from the Best of "ONLINE" [and]"DATABASE."

    ERIC Educational Resources Information Center

    Online, Inc., Weston, CT.

    Reprints of 20 articles pertaining to the topics of end-users and public access appear in this volume, which is one in a series of volumes of reprints from "ONLINE" and "DATABASE" magazines. Edited for information professionals who use electronically distributed databases, these articles address such topics as: (1) managing a compact disc…

  8. 76 FR 53912 - FDA's Public Database of Products With Orphan-Drug Designation: Replacing Non-Informative Code...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-30

    ... HUMAN SERVICES Food and Drug Administration FDA's Public Database of Products With Orphan-Drug... its public database of products that have received orphan-drug designation. The Orphan Drug Act... received orphan designation were published on our public database with non-informative code names....

  9. Bioethical Biobanks: Three Concerns in Designing and Using Law Enforcement DNA Identification Databases

    SciTech Connect

    D.H. Kaye

    2006-10-19

    Federal and state law enforcement authorities have amassed large collections of DNA samples and the identifying profiles derived from them. These databases help to identify the guilty and to exonerate the innocent, but as the databanks grow, so do fears about civil liberties. The research reported here discusses three legal and social policy issues that have been raised in regard to these biobanks—the choice of loci to type for identifying individuals, the indefinite retention of DNA samples, and the use of the DNA samples or the identifying profiles for research purposes. It also considers the possible value of the databases for research into the genetics of human behavior and the ethics of using them for this purpose. It rejects the broad claim that such research is inherently unethical but proposes procedures for ensuring that the value of the proposed research justifies any psychosocial or other risks to the subjects of the research.

  10. DNA banking and DNA databanking: Legal, ethical, and public policy issues

    SciTech Connect

    Reilly, P.R.; McEwen, J.E.; Lawyer, J.D.; Small, D.

    1997-04-30

    The purpose of this research was to provide support to enable the authors to: (1) perform legal and empirical research and critically analyze DNA banking and DNA databanking as those activities are conducted by state forensic laboratories, the military, academic researchers, and commercial enterprises; and (2) develop a broadcast quality educational videotape for viewing by the general public about DNA technology and the privacy and related issues that it raises. The grant thus had both a research and analysis component and a public education component. This report outlines the work completed under the project.

  11. The mitochondrial DNA makeup of Romanians: A forensic mtDNA control region database and phylogenetic characterization.

    PubMed

    Turchi, Chiara; Stanciu, Florin; Paselli, Giorgia; Buscemi, Loredana; Parson, Walther; Tagliabracci, Adriano

    2016-09-01

    To evaluate the pattern of Romanian population from a mitochondrial perspective and to establish an appropriate mtDNA forensic database, we generated a high-quality mtDNA control region dataset from 407 Romanian subjects belonging to four major historical regions: Moldavia, Transylvania, Wallachia and Dobruja. The entire control region (CR) was analyzed by Sanger-type sequencing assays and the resulting 306 different haplotypes were classified into haplogroups according to the most updated mtDNA phylogeny. The Romanian gene pool is mainly composed of West Eurasian lineages H (31.7%), U (12.8%), J (10.8%), R (10.1%), T (9.1%), N (8.1%), HV (5.4%),K (3.7%), HV0 (4.2%), with exceptions of East Asian haplogroup M (3.4%) and African haplogroup L (0.7%). The pattern of mtDNA variation observed in this study indicates that the mitochondrial DNA pool is geographically homogeneous across Romania and that the haplogroup composition reveals signals of admixture of populations of different origin. The PCA scatterplot supported this scenario, with Romania located in southeastern Europe area, close to Bulgaria and Hungary, and as a borderland with respect to east Mediterranean and other eastern European countries. High haplotype diversity (0.993) and nucleotide diversity indices (0.00838±0.00426), together with low random match probability (0.0087) suggest the usefulness of this control region dataset as a forensic database in routine forensic mtDNA analysis and in the investigation of maternal genetic lineages in the Romanian population. PMID:27414754

  12. An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

    SciTech Connect

    AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

    2015-11-19

    Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database in which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the

  13. An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

    DOE PAGESBeta

    AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

    2015-11-19

    Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database inmore » which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the

  14. Internet-Accessible DNA Sequence Database for Identifying Fusaria from Human and Animal Infections ▿

    PubMed Central

    O'Donnell, Kerry; Sutton, Deanna A.; Rinaldi, Michael G.; Sarver, Brice A. J.; Balajee, S. Arunmozhi; Schroers, Hans-Josef; Summerbell, Richard C.; Robert, Vincent A. R. G.; Crous, Pedro W.; Zhang, Ning; Aoki, Takayuki; Jung, Kyongyong; Park, Jongsun; Lee, Yong-Hwan; Kang, Seogchan; Park, Bongsoo; Geiser, David M.

    2010-01-01

    Because less than one-third of clinically relevant fusaria can be accurately identified to species level using phenotypic data (i.e., morphological species recognition), we constructed a three-locus DNA sequence database to facilitate molecular identification of the 69 Fusarium species associated with human or animal mycoses encountered in clinical microbiology laboratories. The database comprises partial sequences from three nuclear genes: translation elongation factor 1α (EF-1α), the largest subunit of RNA polymerase (RPB1), and the second largest subunit of RNA polymerase (RPB2). These three gene fragments can be amplified by PCR and sequenced using primers that are conserved across the phylogenetic breadth of Fusarium. Phylogenetic analyses of the combined data set reveal that, with the exception of two monotypic lineages, all clinically relevant fusaria are nested in one of eight variously sized and strongly supported species complexes. The monophyletic lineages have been named informally to facilitate communication of an isolate's clade membership and genetic diversity. To identify isolates to the species included within the database, partial DNA sequence data from one or more of the three genes can be used as a BLAST query against the database which is Web accessible at FUSARIUM-ID (http://isolate.fusariumdb.org) and the Centraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Center (http://www.cbs.knaw.nl/fusarium). Alternatively, isolates can be identified via phylogenetic analysis by adding sequences of unknowns to the DNA sequence alignment, which can be downloaded from the two aforementioned websites. The utility of this database should increase significantly as members of the clinical microbiology community deposit in internationally accessible culture collections (e.g., CBS-KNAW or the Fusarium Research Center) cultures of novel mycosis-associated fusaria, along with associated, corrected sequence chromatograms and data, so that the

  15. Internet-accessible DNA sequence database for identifying fusaria from human and animal infections.

    PubMed

    O'Donnell, Kerry; Sutton, Deanna A; Rinaldi, Michael G; Sarver, Brice A J; Balajee, S Arunmozhi; Schroers, Hans-Josef; Summerbell, Richard C; Robert, Vincent A R G; Crous, Pedro W; Zhang, Ning; Aoki, Takayuki; Jung, Kyongyong; Park, Jongsun; Lee, Yong-Hwan; Kang, Seogchan; Park, Bongsoo; Geiser, David M

    2010-10-01

    Because less than one-third of clinically relevant fusaria can be accurately identified to species level using phenotypic data (i.e., morphological species recognition), we constructed a three-locus DNA sequence database to facilitate molecular identification of the 69 Fusarium species associated with human or animal mycoses encountered in clinical microbiology laboratories. The database comprises partial sequences from three nuclear genes: translation elongation factor 1α (EF-1α), the largest subunit of RNA polymerase (RPB1), and the second largest subunit of RNA polymerase (RPB2). These three gene fragments can be amplified by PCR and sequenced using primers that are conserved across the phylogenetic breadth of Fusarium. Phylogenetic analyses of the combined data set reveal that, with the exception of two monotypic lineages, all clinically relevant fusaria are nested in one of eight variously sized and strongly supported species complexes. The monophyletic lineages have been named informally to facilitate communication of an isolate's clade membership and genetic diversity. To identify isolates to the species included within the database, partial DNA sequence data from one or more of the three genes can be used as a BLAST query against the database which is Web accessible at FUSARIUM-ID (http://isolate.fusariumdb.org) and the Centraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Center (http://www.cbs.knaw.nl/fusarium). Alternatively, isolates can be identified via phylogenetic analysis by adding sequences of unknowns to the DNA sequence alignment, which can be downloaded from the two aforementioned websites. The utility of this database should increase significantly as members of the clinical microbiology community deposit in internationally accessible culture collections (e.g., CBS-KNAW or the Fusarium Research Center) cultures of novel mycosis-associated fusaria, along with associated, corrected sequence chromatograms and data, so that the

  16. From metaphor to practices: The introduction of "information engineers" into the first DNA sequence database.

    PubMed

    García-Sancho, Miguel

    2011-01-01

    This paper explores the introduction of professional systems engineers and information management practices into the first centralized DNA sequence database, developed at the European Molecular Biology Laboratory (EMBL) during the 1980s. In so doing, it complements the literature on the emergence of an information discourse after World War II and its subsequent influence in biological research. By the careers of the database creators and the computer algorithms they designed, analyzing, from the mid-1960s onwards information in biology gradually shifted from a pervasive metaphor to be embodied in practices and professionals such as those incorporated at the EMBL. I then investigate the reception of these database professionals by the EMBL biological staff, which evolved from initial disregard to necessary collaboration as the relationship between DNA, genes, and proteins turned out to be more complex than expected. The trajectories of the database professionals at the EMBL suggest that the initial subject matter of the historiography of genomics should be the long-standing practices that emerged after World War II and to a large extent originated outside biomedicine and academia. Only after addressing these practices, historians may turn to their further disciplinary assemblage in fields such as bioinformatics or biotechnology. PMID:21789956

  17. "Would you accept having your DNA profile inserted in the National Forensic DNA database? Why?" Results of a questionnaire applied in Portugal.

    PubMed

    Machado, Helena; Silva, Susana

    2014-01-01

    The creation and expansion of forensic DNA databases might involve potential threats to the protection of a range of human rights. At the same time, such databases have social benefits. Based on data collected through an online questionnaire applied to 628 individuals in Portugal, this paper aims to analyze the citizens' willingness to donate voluntarily a sample for profiling and inclusion in the National Forensic DNA Database and the views underpinning such a decision. Nearly one-quarter of the respondents would indicate 'no', and this negative response increased significantly with age and education. The overriding willingness to accept the inclusion of the individual genetic profile indicates an acknowledgement of the investigative potential of forensic DNA technologies and a relegation of civil liberties and human rights to the background, owing to the perceived benefits of protecting both society and the individual from crime. This rationale is mostly expressed by the idea that all citizens should contribute to the expansion of the National Forensic DNA Database for reasons that range from the more abstract assumption that donating a sample for profiling would be helpful in fighting crime to the more concrete suggestion that everyone (criminals and non-criminals) should be in the database. The concerns with the risks of accepting the donation of a sample for genetic profiling and inclusion in the National Forensic DNA Database are mostly related to lack of control and insufficient or unclear regulations concerning safeguarding individuals' data and supervising the access and uses of genetic data. By providing an empirically-grounded understanding of the attitudes regarding willingness to donate voluntary a sample for profiling and inclusion in a National Forensic DNA Database, this study also considers the citizens' perceived benefits and risks of operating forensic DNA databases. These collective views might be useful for the formation of international common

  18. The annotation and the usage of scientific databases could be improved with public issue tracker software

    PubMed Central

    Dall'Olio, Giovanni Marco; Bertranpetit, Jaume; Laayouni, Hafid

    2010-01-01

    Since the publication of their longtime predecessor The Atlas of Protein Sequences and Structures in 1965 by Margaret Dayhoff, scientific databases have become a key factor in the organization of modern science. All the information and knowledge described in the novel scientific literature is translated into entries in many different scientific databases, making it possible to obtain very accurate information on a biological entity like genes or proteins without having to manually review the literature on it. However, even for the databases with the finest annotation procedures, errors or unclear parts sometimes appear in the publicly released version and influence the research of unaware scientists using them. The researcher that finds an error in a database is often left in a uncertain state, and often abandons the effort of reporting it because of a lack of a standard procedure to do so. In the present work, we propose that the simple adoption of a public error tracker application, as in many open software projects, could improve the quality of the annotations in many databases and encourage feedback from the scientific community on the data annotated publicly. In order to illustrate the situation, we describe a series of errors that we found and helped solve on the genes of a very well-known pathway in various biomedically relevant databases. We would like to show that, even if a majority of the most important scientific databases have procedures for reporting errors, these are usually not publicly visible, making the process of reporting errors time consuming and not useful. Also, the effort made by the user that reports the error often goes unacknowledged, putting him in a discouraging position. PMID:21186182

  19. HUGE: a database for human large proteins identified in the Kazusa cDNA sequencing project.

    PubMed

    Kikuno, R; Nagase, T; Suyama, M; Waki, M; Hirosawa, M; Ohara, O

    2000-01-01

    HUGE is a database for human large proteins newly identified in the Kazusa cDNA project, the aim of which is to predict the primary structure of proteins from the sequences of human large cDNAs (>4 kb). In particular, cDNA clones capable of coding for large proteins (>50 kDa) are the current targets of the project. HUGE contains >1100 cDNA sequences and detailed information obtained through analysis of the sequences of cDNAs and the predicted proteins. Besides an increase in the number of cDNA entries, the amount of experimental data for expression profiling has been largely increased and data on chromosomal locations have been newly added. All of the protein-coding regions were examined by GeneMark analysis, and the results of a motif/domain search of each predicted protein sequence against the Pfam database have been newly added. HUGE is available through the WWW at http://www.kazusa.or.jp/huge PMID:10592264

  20. Inspecting close maternal relatedness: Towards better mtDNA population samples in forensic databases

    PubMed Central

    Bodner, Martin; Irwin, Jodi A.; Coble, Michael D.; Parson, Walther

    2011-01-01

    Reliable data are crucial for all research fields applying mitochondrial DNA (mtDNA) as a genetic marker. Quality control measures have been introduced to ensure the highest standards in sequence data generation, validation and a posteriori inspection. A phylogenetic alignment strategy has been widely accepted as a prerequisite for data comparability and database searches, for forensic applications, for reconstructions of human migrations and for correct interpretation of mtDNA mutations in medical genetics. There is continuing effort to enhance the number of worldwide population samples in order to contribute to a better understanding of human mtDNA variation. This has often lead to the analysis of convenience samples collected for other purposes, which might not meet the quality requirement of random sampling for mtDNA data sets. Here, we introduce an additional quality control means that deals with one aspect of this limitation: by combining autosomal short tandem repeat (STR) marker with mtDNA information, it helps to avoid the bias introduced by related individuals included in the same (small) sample. By STR analysis of individuals sharing their mitochondrial haplotype, pedigree construction and subsequent software-assisted calculation of likelihood ratios based on the allele frequencies found in the population, closely maternally related individuals can be identified and excluded. We also discuss scenarios that allow related individuals in the same set. An ideal population sample would be representative for its population: this new approach represents another contribution towards this goal. PMID:21067986

  1. Inspecting close maternal relatedness: Towards better mtDNA population samples in forensic databases.

    PubMed

    Bodner, Martin; Irwin, Jodi A; Coble, Michael D; Parson, Walther

    2011-03-01

    Reliable data are crucial for all research fields applying mitochondrial DNA (mtDNA) as a genetic marker. Quality control measures have been introduced to ensure the highest standards in sequence data generation, validation and a posteriori inspection. A phylogenetic alignment strategy has been widely accepted as a prerequisite for data comparability and database searches, for forensic applications, for reconstructions of human migrations and for correct interpretation of mtDNA mutations in medical genetics. There is continuing effort to enhance the number of worldwide population samples in order to contribute to a better understanding of human mtDNA variation. This has often lead to the analysis of convenience samples collected for other purposes, which might not meet the quality requirement of random sampling for mtDNA data sets. Here, we introduce an additional quality control means that deals with one aspect of this limitation: by combining autosomal short tandem repeat (STR) marker with mtDNA information, it helps to avoid the bias introduced by related individuals included in the same (small) sample. By STR analysis of individuals sharing their mitochondrial haplotype, pedigree construction and subsequent software-assisted calculation of likelihood ratios based on the allele frequencies found in the population, closely maternally related individuals can be identified and excluded. We also discuss scenarios that allow related individuals in the same set. An ideal population sample would be representative for its population: this new approach represents another contribution towards this goal. PMID:21067986

  2. Development and Evaluation of a Quality-Controlled Ribosomal Sequence Database for 16S Ribosomal DNA-Based Identification of Staphylococcus Species

    PubMed Central

    Becker, Karsten; Harmsen, Dag; Mellmann, Alexander; Meier, Christian; Schumann, Peter; Peters, Georg; von Eiff, Christof

    2004-01-01

    To establish an improved ribosomal gene sequence database as part of the Ribosomal Differentiation of Microorganisms (RIDOM) project and to overcome the drawbacks of phenotypic identification systems and publicly accessible sequence databases, both strands of the 5′ end of the 16S ribosomal DNA (rDNA) of 81 type and reference strains comprising all validly described staphylococcal (sub)species were sequenced. Assuming a normal distribution for pairwise distances of all unique staphylococcal sequences and choosing a reporting criterion of ≥98.7% similarity for a “distinct species,” a statistical error probability of 1.0% was calculated. To evaluate this database, a 16S rDNA fragment (corresponding to Escherichia coli positions 54 to 510) of 55 clinical Staphylococcus isolates (including those of the small-colony variant phenotype) were sequenced and analyzed by the RIDOM approach. Of these isolates, 54 (98.2%) had a similarity score above the proposed threshold using RIDOM; 48 (87.3%) of the sequences gave a perfect match, whereas 83.6% were found by searching National Center for Biotechnology Information (NCBI) database entries. In contrast to RIDOM, which showed four ambiguities at the species level (mainly concerning Staphylococcus intermedius versus Staphylococcus delphini), the NCBI database search yielded 18 taxon-related ambiguities and showed numerous matches exhibiting redundant or unspecified entries. Comparing molecular results with those of biochemical procedures, ID 32 Staph (bioMérieux, Marcy I'Etoile, France) and VITEK 2 (bioMérieux) failed to identify 13 (23.6%) and 19 (34.5%) isolates, respectively, due to incorrect identification and/or categorization below acceptable values. In contrast to phenotypic methods and the NCBI database, the novel high-quality RIDOM sequence database provides excellent identification of staphylococci, including rarely isolated species and phenotypic variants. PMID:15528685

  3. PUBLIC HEALTH AND EPIDEMIOLOGICAL DATABASES FOR THE ENHANCEMENT OF MEDICAL EDUCATION

    PubMed Central

    Jamal, Qazi Mohammad Sajid; Siddiqui, Mughees Uddin; Alzohairy, Mohammad Abdulrahman; Al Karaawi, Mohammed Abdullah

    2015-01-01

    The collaboration of public health education and information technology has made patient care safer and more reliable than before. Nurses and doctors use handheld computers to record a patient's medical history and check that they are administering the correct treatment. Fortunately Public Health Informatics (PHI) is the intersecting point of technology and public health. Therefore, the inclusion of online medical and epidemiology databases in the course curriculum of budding medical professionals and postgraduate students would be beneficial in enhancing the quality of health care, extensive epidemiological research, health education, health policies, health planning and consumer satisfaction as well. The purpose of this article is to discuss and provide introduction of various databases which have huge information and it could be used to enhance the public health education. PMID:26392847

  4. PUBLIC HEALTH AND EPIDEMIOLOGICAL DATABASES FOR THE ENHANCEMENT OF MEDICAL EDUCATION.

    PubMed

    Jamal, Qazi Mohammad Sajid; Siddiqui, Mughees Uddin; Alzohairy, Mohammad Abdulrahman; Al Karaawi, Mohammed Abdullah

    2015-01-01

    The collaboration of public health education and information technology has made patient care safer and more reliable than before. Nurses and doctors use handheld computers to record a patient's medical history and check that they are administering the correct treatment. Fortunately Public Health Informatics (PHI) is the intersecting point of technology and public health. Therefore, the inclusion of online medical and epidemiology databases in the course curriculum of budding medical professionals and postgraduate students would be beneficial in enhancing the quality of health care, extensive epidemiological research, health education, health policies, health planning and consumer satisfaction as well. The purpose of this article is to discuss and provide introduction of various databases which have huge information and it could be used to enhance the public health education. PMID:26392847

  5. The Neutron Monitor database as a tool for space weather, education, and public outreach

    NASA Astrophysics Data System (ADS)

    Steigies, Christian T.; Klein, Karl-Ludwig; Bütikofer, Rolf

    2014-05-01

    The Neutron Monitor database (NMDB) was created to make measurements from ground-based Neutron Monitors easily accessible. Data from more than 40 stations is available in the database and can be plotted via a webpage and downloaded as ASCII tables for further processing. Real-time applications, like the GLE Alert, can access the database directly. The NMDB project has also hosted training sessions and created extensive public outreach and training material that has been translated into 11 languages. This material is openly available on the NMDB website and is frequently used in highschool and university courses. While the availability of data from currently operating stations is nearing completion, the availability of historical data, especially no longer operating stations, is still limited. We are currently trying to fill these gaps. As a first step a project to make NMDB compatible with the database of relativistic solar particle events (GLEs) is starting this year.

  6. HEDS - EPA DATABASE SYSTEM FOR PUBLIC ACCESS TO HUMAN EXPOSURE DATA

    EPA Science Inventory

    Human Exposure Database System (HEDS) is an Internet-based system developed to provide public access to human-exposure-related data from studies conducted by EPA's National Exposure Research Laboratory (NERL). HEDS was designed to work with the EPA Office of Research and Devel...

  7. Governing Software: Networks, Databases and Algorithmic Power in the Digital Governance of Public Education

    ERIC Educational Resources Information Center

    Williamson, Ben

    2015-01-01

    This article examines the emergence of "digital governance" in public education in England. Drawing on and combining concepts from software studies, policy and political studies, it identifies some specific approaches to digital governance facilitated by network-based communications and database-driven information processing software…

  8. An efficient similarity search based on indexing in large DNA databases.

    PubMed

    Jeong, In-Seon; Park, Kyoung-Wook; Kang, Seung-Ho; Lim, Hyeong-Seok

    2010-04-01

    Index-based search algorithms are an important part of a genomic search, and how to construct indices is the key to an index-based search algorithm to compute similarities between two DNA sequences. In this paper, we propose an efficient query processing method that uses special transformations to construct an index. It uses small storage and it rapidly finds the similarity between two sequences in a DNA sequence database. At first, a sequence is partitioned into equal length windows. We select the likely subsequences by computing Hamming distance to query sequence. The algorithm then transforms the subsequences in each window into a multidimensional vector space by indexing the frequencies of the characters, including the positional information of the characters in the subsequences. The result of our experiments shows that the algorithm has faster run time than other heuristic algorithms based on index structure. Also, the algorithm is as accurate as those heuristic algorithms. PMID:20418167

  9. A PCR multiplex and database for forensic DNA identification of dogs.

    PubMed

    Halverson, Joy; Basten, Christopher

    2005-03-01

    Animal-derived trace evidence is a common finding at crime scenes and may provide an important link between victim(s) and suspect(s). A database of 558 dogs of pure and mixed breeds is described and analyzed with two PCR multiplexes of 17 microsatellites. Summary statistics (number of alleles, expected and observed heterozygosity and power of exclusion) are compared between breeds. Marked population substructure in dog breeds indicates significant inbreeding, and the use of a conservative theta value is recommended in likelihood calculations for determining the significance of a DNA match. Evidence is presented that the informativeness of the canine microsatellites, despite inbreeding, is comparable to the human CODIS loci. Two cases utilizing canine DNA typing, State of Washington v. Kenneth Leuluaialii and George Tuilefano and Crown v. Daniel McGowan, illustrate the potential of canine microsatellite markers for forensic investigations. PMID:15813546

  10. Development of a Publicly Available, Comprehensive Database of Fiber and Health Outcomes: Rationale and Methods

    PubMed Central

    Livingston, Kara A.; Chung, Mei; Sawicki, Caleigh M.; Lyle, Barbara J.; Wang, Ding Ding; Roberts, Susan B.; McKeown, Nicola M.

    2016-01-01

    Background Dietary fiber is a broad category of compounds historically defined as partially or completely indigestible plant-based carbohydrates and lignin with, more recently, the additional criteria that fibers incorporated into foods as additives should demonstrate functional human health outcomes to receive a fiber classification. Thousands of research studies have been published examining fibers and health outcomes. Objectives (1) Develop a database listing studies testing fiber and physiological health outcomes identified by experts at the Ninth Vahouny Conference; (2) Use evidence mapping methodology to summarize this body of literature. This paper summarizes the rationale, methodology, and resulting database. The database will help both scientists and policy-makers to evaluate evidence linking specific fibers with physiological health outcomes, and identify missing information. Methods To build this database, we conducted a systematic literature search for human intervention studies published in English from 1946 to May 2015. Our search strategy included a broad definition of fiber search terms, as well as search terms for nine physiological health outcomes identified at the Ninth Vahouny Fiber Symposium. Abstracts were screened using a priori defined eligibility criteria and a low threshold for inclusion to minimize the likelihood of rejecting articles of interest. Publications then were reviewed in full text, applying additional a priori defined exclusion criteria. The database was built and published on the Systematic Review Data Repository (SRDR™), a web-based, publicly available application. Conclusions A fiber database was created. This resource will reduce the unnecessary replication of effort in conducting systematic reviews by serving as both a central database archiving PICO (population, intervention, comparator, outcome) data on published studies and as a searchable tool through which this data can be extracted and updated. PMID:27348733

  11. Misguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databases.

    PubMed

    Pylro, Victor Satler; Morais, Daniel Kumazawa; Kalks, Karlos Henrique Martins; Roesch, Luiz Fernando Wurdig; Hirsch, Penny R; Tótola, Marcos Rogério; Yotoko, Karla

    2016-07-01

    Controversy surrounding bacterial phylogenies has become one of the most important challenges for microbial ecology. Comparative analyses with nucleotide databases and phylogenetic reconstruction of the amplified 16S rRNA genes from DGGE (Denaturing Gradient Gel Electrophoresis) excised bands have been used by several researchers for the identification of organisms in complex samples. Here, we individually analyzed DGGE-excised 16S rRNA gene bands from 10 certified bacterial strains of different species, and demonstrated that this kind of approach can deliver erroneous outcomes to researchers, besides causing/emphasizing errors in public databases. PMID:27109483

  12. 76 FR 77533 - Notice of Order: Revisions to Enterprise Public Use Database Incorporating High-Cost Single...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-13

    ... September 28, 2011 at 76 FR 60031, regarding FHFA's adoption of an Order revising FHFA's Public Use Database... From the Federal Register Online via the Government Publishing Office FEDERAL HOUSING FINANCE AGENCY Notice of Order: Revisions to Enterprise Public Use Database Incorporating High-Cost...

  13. Effect of reference database on frequency estimates of polymerase chain reaction (PCR)-based DNA profiles.

    PubMed

    Monson, K L; Budowle, B

    1998-05-01

    A variety of general, regional, ancestral and ethnic databases is available for the polymerase chain reaction (PCR)-based loci LDLR, GYPA, HBGG, D7S8, Gc, DQA1, and D1S80. Generally, we observed greater differences in frequency estimations of DNA profiles between racial groups than between ethnic or geographic subgroups. Analysis revealed few forensically significant differences within ethnic subgroups, particularly within general United States groups, and multi-locus frequency estimates typically differ by less than a factor of ten. Using a database different from the one to which a target profile belongs tends to overestimate rarity. Implementation of the general correction of homozygote frequencies for a population substructure, advised by the 1996 National Research Council report, The Evaluation of Forensic DNA Evidence, has a minimal effect on profile frequencies. Even when it is known that both the suspect and all possible perpetrators must belong to the same isolated population, the special correction for inbreeding, which was proposed by the 1996 National Research Council report for this special case, has a relatively modest effect, typically a factor of two or less for 1% inbreeding. The effect becomes more substantial (exceeding a factor of ten) for inbreeding of 3% or more in multi-locus profiles rarer than about one in a million. PMID:9608687

  14. Approaching the taxonomic affiliation of unidentified sequences in public databases – an example from the mycorrhizal fungi

    PubMed Central

    Nilsson, R Henrik; Kristiansson, Erik; Ryberg, Martin; Larsson, Karl-Henrik

    2005-01-01

    Background During the last few years, DNA sequence analysis has become one of the primary means of taxonomic identification of species, particularly so for species that are minute or otherwise lack distinct, readily obtainable morphological characters. Although the number of sequences available for comparison in public databases such as GenBank increases exponentially, only a minuscule fraction of all organisms have been sequenced, leaving taxon sampling a momentous problem for sequence-based taxonomic identification. When querying GenBank with a set of unidentified sequences, a considerable proportion typically lack fully identified matches, forming an ever-mounting pile of sequences that the researcher will have to monitor manually in the hope that new, clarifying sequences have been submitted by other researchers. To alleviate these concerns, a project to automatically monitor select unidentified sequences in GenBank for taxonomic progress through repeated local BLAST searches was initiated. Mycorrhizal fungi – a field where species identification often is prohibitively complex – and the much used ITS locus were chosen as test bed. Results A Perl script package called emerencia is presented. On a regular basis, it downloads select sequences from GenBank, separates the identified sequences from those insufficiently identified, and performs BLAST searches between these two datasets, storing all results in an SQL database. On the accompanying web-service , users can monitor the taxonomic progress of insufficiently identified sequences over time, either through active searches or by signing up for e-mail notification upon disclosure of better matches. Other search categories, such as listing all insufficiently identified sequences (and their present best fully identified matches) publication-wise, are also available. Discussion The ever-increasing use of DNA sequences for identification purposes largely falls back on the assumption that public sequence databases

  15. Government databases and public health research: facilitating access in the public interest.

    PubMed

    Adams, Carolyn; Allen, Judy

    2014-06-01

    Access to datasets of personal health information held by government agencies is essential to support public health research and to promote evidence-based public health policy development. Privacy legislation in Australia allows the use and disclosure of such information for public health research. However, access is not always forthcoming in a timely manner and the decision-making process undertaken by government data custodians is not always transparent. Given the public benefit in research using these health information datasets, this article suggests that it is time to recognise a right of access for approved research and that the decisions, and decision-making processes, of government data custodians should be subject to increased scrutiny. The article concludes that researchers should have an avenue of external review where access to information has been denied or unduly delayed. PMID:25087372

  16. A Large Population Genetic Study of 15 Autosomal Short Tandem Repeat Loci for Establishment of Korean DNA Profile Database

    PubMed Central

    Yoo, Seong Yeon; Cho, Nam Soo; Park, Myung Jin; Seong, Ki Min; Hwang, Jung Ho; Song, Seok Bean; Han, Myun Soo; Lee, Won Tae; Chung, Ki Wha

    2011-01-01

    Genotyping of highly polymorphic short tandem repeat (STR) markers is widely used for the genetic identification of individuals in forensic DNA analyses and in paternity disputes. The National DNA Profile Databank recently established by the DNA Identification Act in Korea contains the computerized STR DNA profiles of individuals convicted of crimes. For the establishment of a large autosomal STR loci population database, 1805 samples were obtained at random from Korean individuals and 15 autosomal STR markers were analyzed using the AmpFlSTR Identifiler PCR Amplification kit. For the 15 autosomal STR markers, no deviations from the Hardy-Weinberg equilibrium were observed. The most informative locus in our data set was the D2S1338 with a discrimination power of 0.9699. The combined matching probability was 1.521 × 10-17. This large STR profile dataset including atypical alleles will be important for the establishment of the Korean DNA database and for forensic applications. PMID:21597912

  17. Recommendations of the DNA Commission of the International Society for Forensic Genetics (ISFG) on quality control of autosomal Short Tandem Repeat allele frequency databasing (STRidER).

    PubMed

    Bodner, Martin; Bastisch, Ingo; Butler, John M; Fimmers, Rolf; Gill, Peter; Gusmão, Leonor; Morling, Niels; Phillips, Christopher; Prinz, Mechthild; Schneider, Peter M; Parson, Walther

    2016-09-01

    The statistical evaluation of autosomal Short Tandem Repeat (STR) genotypes is based on allele frequencies. These are empirically determined from sets of randomly selected human samples, compiled into STR databases that have been established in the course of population genetic studies. There is currently no agreed procedure of performing quality control of STR allele frequency databases, and the reliability and accuracy of the data are largely based on the responsibility of the individual contributing research groups. It has been demonstrated with databases of haploid markers (EMPOP for mitochondrial mtDNA, and YHRD for Y-chromosomal loci) that centralized quality control and data curation is essential to minimize error. The concepts employed for quality control involve software-aided likelihood-of-genotype, phylogenetic, and population genetic checks that allow the researchers to compare novel data to established datasets and, thus, maintain the high quality required in forensic genetics. Here, we present STRidER (http://strider.online), a publicly available, centrally curated online allele frequency database and quality control platform for autosomal STRs. STRidER expands on the previously established ENFSI DNA WG STRbASE and applies standard concepts established for haploid and autosomal markers as well as novel tools to reduce error and increase the quality of autosomal STR data. The platform constitutes a significant improvement and innovation for the scientific community, offering autosomal STR data quality control and reliable STR genotype estimates. PMID:27352221

  18. SITVITWEB--a publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology.

    PubMed

    Demay, Christophe; Liens, Benjamin; Burguière, Thomas; Hill, Véronique; Couvin, David; Millet, Julie; Mokrousov, Igor; Sola, Christophe; Zozio, Thierry; Rastogi, Nalin

    2012-06-01

    Among various genotyping methods to study Mycobacterium tuberculosis complex (MTC) genotypic polymorphism, spoligotyping and mycobacterial interspersed repetitive units-variable number of DNA tandem repeats (MIRU-VNTRs) have recently gained international approval as robust, fast, and reproducible typing methods generating data in a portable format. Spoligotyping constituted the backbone of a publicly available database SpolDB4 released in 2006; nonetheless this method possesses a low discriminatory power when used alone and should be ideally used in conjunction with a second typing method such as MIRU-VNTRs for high-resolution epidemiological studies. We hereby describe a publicly available international database named SITVITWEB which incorporates such multimarker data allowing to have a global vision of MTC genetic diversity worldwide based on 62,582 clinical isolates corresponding to 153 countries of patient origin (105 countries of isolation). We report a total of 7105 spoligotype patterns (corresponding to 58,180 clinical isolates) - grouped into 2740 shared-types or spoligotype international types (SIT) containing 53,816 clinical isolates and 4364 orphan patterns. Interestingly, only 7% of the MTC isolates worldwide were orphans whereas more than half of SITed isolates (n=27,059) were restricted to only 24 most prevalent SITs. The database also contains a total of 2379 MIRU patterns (from 8161 clinical isolates) from 87 countries of patient origin (35 countries of isolation); these were grouped in 847 shared-types or MIRU international types (MIT) containing 6626 isolates and 1533 orphan patterns. Lastly, data on 5-locus exact tandem repeats (ETRs) were available on 4626 isolates from 59 countries of patient origin (22 countries of isolation); a total of 458 different VNTR patterns were observed - split into 245 shared-types or VNTR International Types (VIT) containing 4413 isolates) and 213 orphan patterns. Datamining of SITVITWEB further allowed to update

  19. Generation and analysis of end sequence database for T-DNA tagging lines in rice.

    PubMed

    An, Suyoung; Park, Sunhee; Jeong, Dong-Hoon; Lee, Dong-Yeon; Kang, Hong-Gyu; Yu, Jung-Hwa; Hur, Junghe; Kim, Sung-Ryul; Kim, Young-Hea; Lee, Miok; Han, Soonki; Kim, Soo-Jin; Yang, Jungwon; Kim, Eunjoo; Wi, Soo Jin; Chung, Hoo Sun; Hong, Jong-Pil; Choe, Vitnary; Lee, Hak-Kyung; Choi, Jung-Hee; Nam, Jongmin; Kim, Seong-Ryong; Park, Phun-Bum; Park, Ky Young; Kim, Woo Taek; Choe, Sunghwa; Lee, Chin-Bum; An, Gynheung

    2003-12-01

    We analyzed 6749 lines tagged by the gene trap vector pGA2707. This resulted in the isolation of 3793 genomic sequences flanking the T-DNA. Among the insertions, 1846 T-DNAs were integrated into genic regions, and 1864 were located in intergenic regions. Frequencies were also higher at the beginning and end of the coding regions and upstream near the ATG start codon. The overall GC content at the insertion sites was close to that measured from the entire rice (Oryza sativa) genome. Functional classification of these 1846 tagged genes showed a distribution similar to that observed for all the genes in the rice chromosomes. This indicates that T-DNA insertion is not biased toward a particular class of genes. There were 764, 327, and 346 T-DNA insertions in chromosomes 1, 4 and 10, respectively. Insertions were not evenly distributed; frequencies were higher at the ends of the chromosomes and lower near the centromere. At certain sites, the frequency was higher than in the surrounding regions. This sequence database will be valuable in identifying knockout mutants for elucidating gene function in rice. This resource is available to the scientific community at http://www.postech.ac.kr/life/pfg/risd. PMID:14630961

  20. Applying Knowledge Discovery in Databases in Public Health Data Set: Challenges and Concerns

    PubMed Central

    Volrathongchia, Kanittha

    2003-01-01

    In attempting to apply Knowledge Discovery in Databases (KDD) to generate a predictive model from a health care dataset that is currently available to the public, the first step is to pre-process the data to overcome the challenges of missing data, redundant observations, and records containing inaccurate data. This study will demonstrate how to use simple pre-processing methods to improve the quality of input data. PMID:14728545

  1. Update of AMmtDB: a database of multi-aligned Metazoa mitochondrial DNA sequences.

    PubMed

    Lanave, Cecilia; Licciulli, Flavio; De Robertis, Mariateresa; Marolla, Alessandra; Attimonelli, Marcella

    2002-01-01

    The AMmtDB database (http://bighost.area.ba.cnr.it/mitochondriome) has been updated by collecting the multi-aligned sequences of Chordata and Invertebrata mitochondrial genes coding for proteins and tRNAs. Links to the multi-aligned mtDNA intraspecies variants, collected in VarMmtDB at the Mitochondriome web site, have been introduced. The genes coding for proteins are multi-aligned based on the translated sequences and both the nucleotide and amino acid multi-alignments are provided. AMmtDB data selected through SRS can be viewed and managed using GeneDoc or other programs for the management of multi-aligned data depending on the user's operative system. The multiple alignments have been produced with CLUSTALW and PILEUP programs and then carefully optimized manually. PMID:11752285

  2. Update of AMmtDB: a database of multi-aligned Metazoa mitochondrial DNA sequences

    PubMed Central

    Lanave, Cecilia; Licciulli, Flavio; De Robertis, Mariateresa; Marolla, Alessandra; Attimonelli, Marcella

    2002-01-01

    The AMmtDB database (http://bighost.area.ba.cnr.it/mitochondriome) has been updated by collecting the multi-aligned sequences of Chordata and Invertebrata mitochondrial genes coding for proteins and tRNAs. Links to the multi-aligned mtDNA intraspecies variants, collected in VarMmtDB at the Mitochondriome web site, have been introduced. The genes coding for proteins are multi-aligned based on the translated sequences and both the nucleotide and amino acid multi-alignments are provided. AMmtDB data selected through SRS can be viewed and managed using GeneDoc or other programs for the management of multi-aligned data depending on the user’s operative system. The multiple alignments have been produced with CLUSTALW and PILEUP programs and then carefully optimized manually. PMID:11752285

  3. CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state.

    PubMed

    Monzon, Alexander Miguel; Rohr, Cristian Oscar; Fornasari, María Silvina; Parisi, Gustavo

    2016-01-01

    CoDNaS (conformational diversity of the native state) is a protein conformational diversity database. Conformational diversity describes structural differences between conformers that define the native state of proteins. It is a key concept to understand protein function and biological processes related to protein functions. CoDNaS offers a well curated database that is experimentally driven, thoroughly linked, and annotated. CoDNaS facilitates the extraction of key information on small structural differences based on protein movements. CoDNaS enables users to easily relate the degree of conformational diversity with physical, chemical and biological properties derived from experiments on protein structure and biological characteristics. The new version of CoDNaS includes ∼70% of all available protein structures, and new tools have been added that run sequence searches, display structural flexibility profiles and allow users to browse the database for different structural classes. These tools facilitate the exploration of protein conformational diversity and its role in protein function. Database URL:http://ufq.unq.edu.ar/codnas. PMID:27022160

  4. CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state

    PubMed Central

    Monzon, Alexander Miguel; Rohr, Cristian Oscar; Fornasari, María Silvina; Parisi, Gustavo

    2016-01-01

    CoDNaS (conformational diversity of the native state) is a protein conformational diversity database. Conformational diversity describes structural differences between conformers that define the native state of proteins. It is a key concept to understand protein function and biological processes related to protein functions. CoDNaS offers a well curated database that is experimentally driven, thoroughly linked, and annotated. CoDNaS facilitates the extraction of key information on small structural differences based on protein movements. CoDNaS enables users to easily relate the degree of conformational diversity with physical, chemical and biological properties derived from experiments on protein structure and biological characteristics. The new version of CoDNaS includes ∼70% of all available protein structures, and new tools have been added that run sequence searches, display structural flexibility profiles and allow users to browse the database for different structural classes. These tools facilitate the exploration of protein conformational diversity and its role in protein function. Database URL: http://ufq.unq.edu.ar/codnas PMID:27022160

  5. Quantitative assessment of the expanding complementarity between public and commercial databases of bioactive compounds

    PubMed Central

    2009-01-01

    Background Since 2004 public cheminformatic databases and their collective functionality for exploring relationships between compounds, protein sequences, literature and assay data have advanced dramatically. In parallel, commercial sources that extract and curate such relationships from journals and patents have also been expanding. This work updates a previous comparative study of databases chosen because of their bioactive content, availability of downloads and facility to select informative subsets. Results Where they could be calculated, extracted compounds-per-journal article were in the range of 12 to 19 but compound-per-protein counts increased with document numbers. Chemical structure filtration to facilitate standardised comparisons typically reduced source counts by between 5% and 30%. The pair-wise overlaps between 23 databases and subsets were determined, as well as changes between 2006 and 2008. While all compound sets have increased, PubChem has doubled to 14.2 million. The 2008 comparison matrix shows not only overlap but also unique content across all sources. Many of the detailed differences could be attributed to individual strategies for data selection and extraction. While there was a big increase in patent-derived structures entering PubChem since 2006, GVKBIO contains over 0.8 million unique structures from this source. Venn diagrams showed extensive overlap between compounds extracted by independent expert curation from journals by GVKBIO, WOMBAT (both commercial) and BindingDB (public) but each included unique content. In contrast, the approved drug collections from GVKBIO, MDDR (commercial) and DrugBank (public) showed surprisingly low overlap. Aggregating all commercial sources established that while 1 million compounds overlapped with PubChem 1.2 million did not. Conclusion On the basis of chemical structure content per se public sources have covered an increasing proportion of commercial databases over the last two years. However

  6. Update of MmtDB: a Metazoa mitochondrial DNA variants database.

    PubMed Central

    Attimonelli, M; Calò, D; De Montalvo, A; Lanave, C; Sasanelli, D; Tommaseo Ponzetta, M; Saccone, C

    1998-01-01

    The present paper describes the improvements in MmtDB, a specialised database designed to collect Metazoa mitochondrial DNA variants. Priority in the data collection has been given to Metazoa for which a large amount of variants is available, e.g., for humans. Starting from the sequences available in the Nucleotide Sequence Databases, the redundant sequences have been removed and new sequences from other sources have been added. Value-added information is associated to each variant sequence, e.g., analysed region, experimental method, tissue and cell lines, population data, sex, age, family code and information about the variation events (nucleotide position, involved gene, restriction site gain or loss). Cross-references are introduced to the EMBL Data Library, as well as an internal cross-referencing among MmtDB entries according to tissual, heteroplasmic, familiar and aplotypical correlation. Furthermore MmtDB has a new section, AMmtDB: Aligned Metazoan mitochondrial biosequences. MmtDB can be accessed through the World Wide Web at URL http://WWW.ba.cnr.it/[symbol: see text]areamt08/MmtDBWWW.htm PMID:9399815

  7. Similarity landscapes: An improved method for scientific visualization of information from protein and DNA database searches

    SciTech Connect

    Dogget, N.; Myers, G.; Wills, C.J.

    1998-12-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The authors have used computer simulations and examination of a variety of databases to answer questions about a wide range of evolutionary questions. The authors have found that there is a clear distinction in the evolution of HIV-1 and HIV-2, with the former and more virulent virus evolving more rapidly at a functional level. The authors have discovered highly non-random patterns in the evolution of HIV-1 that can be attributed to a variety of selective pressures. In the course of examination of microsatellite DNA (short repeat regions) in microorganisms, the authors have found clear differences between prokaryotes and eukaryotes in their distribution, differences that can be tied to different selective pressures. They have developed a new method (topiary pruning) for enhancing the phylogenetic information contained in DNA sequences. Most recently, the authors have discovered effects in complex rainforest ecosystems that indicate strong frequency-dependent interactions between host species and their parasites, leading to the maintenance of ecosystem variability.

  8. First whole genome based microsatellite DNA marker database of tomato for mapping and variety identification

    PubMed Central

    2013-01-01

    Background The cultivated tomato is second most consumed vegetable of the world and is an important part of a diverse and balanced diet as a rich source of vitamins, minerals, phenolic antioxidants and antioxidant lycopene having anti-cancer properties. To reap benefit of genomics of the domestic tomato (Solanum lycopersicum L.) unravelled by Tomato Genome Consortium (The Tomato Genome Consortium, 2012), the bulk mining of its markers in totality is imperative and critically required. The solgenomics has limited number of microsatellite DNA markers (2867) pertaining to solanaceae family. As these markers are of linkage map having relative distance, the choice of selected markers based on absolute distance as of physical map is missing. Only limited microsatellite markers with limitations are reported for variety identification thus there is a need for more markers supplementing DUS test and also for traceability of product in global market. Description We present here the first whole genome based microsatellite DNA marker database of tomato, TomSatDB (Tomato MicroSatellite Database) with more than 1.4 million markers mined in-silico, using MIcroSAtellite (MISA) tool. To cater the customized needs of wet lab, features with a novelty of an automated primer designing tool is added. TomSatDB (http://cabindb.iasri.res.in/tomsatdb), a user-friendly and freely accessible tool offers chromosome wise as well as location wise search of primers. It is an online relational database based on “three-tier architecture” that catalogues information of microsatellites in MySQL and user-friendly interface developed using PHP (Hypertext Pre Processor). Conclusion Besides abiotic stress, tomato is known to have biotic stress due to its susceptibility over 200 diseases caused by pathogenic fungi, bacteria, viruses and nematodes. These markers are expected to pave the way of germplasm management over abiotic and biotic stress as well as improvement through molecular breeding, leading

  9. Databases of publications and observations as a part of the Crimean Astronomical Virtual Observatory

    NASA Astrophysics Data System (ADS)

    Shlyapnikov, A.; Bondar', N.; Gorbunov, M.

    We describe the main principles of formation of databases (DBs) with information about astronomical objects and their physical characteristics derived from observations obtained at the Crimean Astrophysical Observatory (CrAO) and published in the ``Izvestiya of the CrAO'' and elsewhere. Emphasis is placed on the DBs missing from the most complete global library of catalogs and data tables, VizieR (supported by the Center of Astronomical Data, Strasbourg). We specially consider the problem of forming a digital archive of observational data obtained at the CrAO as an interactive DB related to database objects and publications. We present examples of all our DBs as elements integrated into the Crimean Astronomical Virtual Observatory. We illustrate the work with the CrAO DBs using tools of the International Virtual Observatory: Aladin, VOPlot, VOSpec, in conjunction with the VizieR and Simbad DBs.

  10. A Public Database of Memory and Naive B-Cell Receptor Sequences.

    PubMed

    DeWitt, William S; Lindau, Paul; Snyder, Thomas M; Sherwood, Anna M; Vignali, Marissa; Carlson, Christopher S; Greenberg, Philip D; Duerkopp, Natalie; Emerson, Ryan O; Robins, Harlan S

    2016-01-01

    The vast diversity of B-cell receptors (BCR) and secreted antibodies enables the recognition of, and response to, a wide range of epitopes, but this diversity has also limited our understanding of humoral immunity. We present a public database of more than 37 million unique BCR sequences from three healthy adult donors that is many fold deeper than any existing resource, together with a set of online tools designed to facilitate the visualization and analysis of the annotated data. We estimate the clonal diversity of the naive and memory B-cell repertoires of healthy individuals, and provide a set of examples that illustrate the utility of the database, including several views of the basic properties of immunoglobulin heavy chain sequences, such as rearrangement length, subunit usage, and somatic hypermutation positions and dynamics. PMID:27513338

  11. A Public Database of Memory and Naive B-Cell Receptor Sequences

    PubMed Central

    Sherwood, Anna M.; Vignali, Marissa; Carlson, Christopher S.; Greenberg, Philip D.; Duerkopp, Natalie; Emerson, Ryan O.; Robins, Harlan S.

    2016-01-01

    The vast diversity of B-cell receptors (BCR) and secreted antibodies enables the recognition of, and response to, a wide range of epitopes, but this diversity has also limited our understanding of humoral immunity. We present a public database of more than 37 million unique BCR sequences from three healthy adult donors that is many fold deeper than any existing resource, together with a set of online tools designed to facilitate the visualization and analysis of the annotated data. We estimate the clonal diversity of the naive and memory B-cell repertoires of healthy individuals, and provide a set of examples that illustrate the utility of the database, including several views of the basic properties of immunoglobulin heavy chain sequences, such as rearrangement length, subunit usage, and somatic hypermutation positions and dynamics. PMID:27513338

  12. 76 FR 60031 - Notice of Order: Revisions to Enterprise Public Use Database Incorporating High-Cost Single...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-28

    ... 1, 2010 (75 FR 41180, 41189 (July 15, 2010)) and shall be effective until such time as FHFA... AGENCY Notice of Order: Revisions to Enterprise Public Use Database Incorporating High-Cost Single-Family... Database (PUDB) to include data fields for the high-cost single-family securitized loans data in a...

  13. Fluorescence- and capillary electrophoresis (CE)-based SSR DNA fingerprinting and a molecular identity database for the Louisiana sugarcane industry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A database of Louisiana sugarcane molecular identity has been constructed and is being updated annually using FAM or HEX or NED fluorescence- and capillary electrophoresis (CE)-based microsatellite (SSR) fingerprinting information. The fingerprints are PCR-amplified from leaf DNA samples of current ...

  14. A Two-locus DNA Sequence Database for Typing Plant and Human Pathogens Within the Fusarium oxysporum Species Complex

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We constructed a two-locus database, comprising partial translation elongation factor (EF-1alpha) gene sequences and nearly full-length sequences of the nuclear ribosomal intergenic spacer region (IGS rDNA) for 850 isolates spanning the phylogenetic breadth of the Fusarium oxysporum species complex ...

  15. Database on Danish population-based registers for public health and welfare research.

    PubMed

    Sortsø, Camilla; Thygesen, Lau Caspar; Brønnum-Hansen, Henrik

    2011-07-01

    Population-based studies with information from registers can take place in Denmark due to linkage between registers at the individual level by means of a unique personal identification number (CPR-number), which all persons with residence in Denmark have. Registers with information on health can be linked to other population registers containing information on, for example, transfer payments, education, housing, income, and socioeconomic position. This article introduces a database and search engine, which is available for public health and welfare researchers as an aid to seek information on the content of important Danish registers. PMID:21898917

  16. The Government Finance Database: A Common Resource for Quantitative Research in Public Financial Analysis

    PubMed Central

    Pierson, Kawika; Hand, Michael L.; Thompson, Fred

    2015-01-01

    Quantitative public financial management research focused on local governments is limited by the absence of a common database for empirical analysis. While the U.S. Census Bureau distributes government finance data that some scholars have utilized, the arduous process of collecting, interpreting, and organizing the data has led its adoption to be prohibitive and inconsistent. In this article we offer a single, coherent resource that contains all of the government financial data from 1967-2012, uses easy to understand natural-language variable names, and will be extended when new data is available. PMID:26107821

  17. The Government Finance Database: A Common Resource for Quantitative Research in Public Financial Analysis.

    PubMed

    Pierson, Kawika; Hand, Michael L; Thompson, Fred

    2015-01-01

    Quantitative public financial management research focused on local governments is limited by the absence of a common database for empirical analysis. While the U.S. Census Bureau distributes government finance data that some scholars have utilized, the arduous process of collecting, interpreting, and organizing the data has led its adoption to be prohibitive and inconsistent. In this article we offer a single, coherent resource that contains all of the government financial data from 1967-2012, uses easy to understand natural-language variable names, and will be extended when new data is available. PMID:26107821

  18. MitoAge: a database for comparative analysis of mitochondrial DNA, with a special focus on animal longevity.

    PubMed

    Toren, Dmitri; Barzilay, Thomer; Tacutu, Robi; Lehmann, Gilad; Muradian, Khachik K; Fraifeld, Vadim E

    2016-01-01

    Mitochondria are the only organelles in the animal cells that have their own genome. Due to a key role in energy production, generation of damaging factors (ROS, heat), and apoptosis, mitochondria and mtDNA in particular have long been considered one of the major players in the mechanisms of aging, longevity and age-related diseases. The rapidly increasing number of species with fully sequenced mtDNA, together with accumulated data on longevity records, provides a new fascinating basis for comparative analysis of the links between mtDNA features and animal longevity. To facilitate such analyses and to support the scientific community in carrying these out, we developed the MitoAge database containing calculated mtDNA compositional features of the entire mitochondrial genome, mtDNA coding (tRNA, rRNA, protein-coding genes) and non-coding (D-loop) regions, and codon usage/amino acids frequency for each protein-coding gene. MitoAge includes 922 species with fully sequenced mtDNA and maximum lifespan records. The database is available through the MitoAge website (www.mitoage.org or www.mitoage.info), which provides the necessary tools for searching, browsing, comparing and downloading the data sets of interest for selected taxonomic groups across the Kingdom Animalia. The MitoAge website assists in statistical analysis of different features of the mtDNA and their correlative links to longevity. PMID:26590258

  19. MitoAge: a database for comparative analysis of mitochondrial DNA, with a special focus on animal longevity

    PubMed Central

    Toren, Dmitri; Barzilay, Thomer; Tacutu, Robi; Lehmann, Gilad; Muradian, Khachik K.; Fraifeld, Vadim E.

    2016-01-01

    Mitochondria are the only organelles in the animal cells that have their own genome. Due to a key role in energy production, generation of damaging factors (ROS, heat), and apoptosis, mitochondria and mtDNA in particular have long been considered one of the major players in the mechanisms of aging, longevity and age-related diseases. The rapidly increasing number of species with fully sequenced mtDNA, together with accumulated data on longevity records, provides a new fascinating basis for comparative analysis of the links between mtDNA features and animal longevity. To facilitate such analyses and to support the scientific community in carrying these out, we developed the MitoAge database containing calculated mtDNA compositional features of the entire mitochondrial genome, mtDNA coding (tRNA, rRNA, protein-coding genes) and non-coding (D-loop) regions, and codon usage/amino acids frequency for each protein-coding gene. MitoAge includes 922 species with fully sequenced mtDNA and maximum lifespan records. The database is available through the MitoAge website (www.mitoage.org or www.mitoage.info), which provides the necessary tools for searching, browsing, comparing and downloading the data sets of interest for selected taxonomic groups across the Kingdom Animalia. The MitoAge website assists in statistical analysis of different features of the mtDNA and their correlative links to longevity. PMID:26590258

  20. Reusable data in public health data-bases-problems encountered in Danish Children's Database.

    PubMed

    Høstgaard, Anna Marie; Pape-Haugaard, Louise

    2012-01-01

    Denmark have unique health informatics databases e.g. "The Children's Database", which since 2009 holds data on all Danish children from birth until 17 years of age. In the current set-up a number of potential sources of errors exist - both technical and human-which means that the data is flawed. This gives rise to erroneous statistics and makes the data unsuitable for research purposes. In order to make the data usable, it is necessary to develop new methods for validating the data generation process at the municipal/regional/national level. In the present ongoing research project, two research areas are combined: Public Health Informatics and Computer Science, and both ethnographic as well as system engineering research methods are used. The project is expected to generate new generic methods and knowledge about electronic data collection and transmission in different social contexts and by different social groups and thus to be of international importance, since this is sparsely documented in the Public Health Informatics perspective. This paper presents the preliminary results, which indicate that health information technology used ought to be subject for redesign, where a thorough insight into the work practices should be point of departure. PMID:22874263

  1. Public Perceptions and Expectations of the Forensic Use of DNA: Results of a Preliminary Study

    ERIC Educational Resources Information Center

    Curtis, Cate

    2009-01-01

    The forensic use of Deoxyribonucleic Acid (DNA) is demonstrating significant success as a crime-solving tool. However, numerous concerns have been raised regarding the potential for DNA use to contravene cultural, ethical, and legal codes. In this article the expectations and level of knowledge of the New Zealand public of the DNA data-bank and…

  2. DNA banking and DNA databanking: Legal, ethical, and public policy issues. Progress report, [April 1, 1993--March 31, 1994

    SciTech Connect

    Reilly, P.R.; McEwen, J.E.; Small, D.

    1994-02-18

    The purpose of the grant was to provide support to enable us to: (1) perform legal and empirical research and critically analyze DNA banking and DNA databanking as those activities are conducted by state forensic laboratories, the military, academic researchers, and commercial enterprises; and (2) develop a broadcast quality educational videotape for viewing by the general public about DNA technology and the privacy and related issues that it raises. The grant thus has both a research and analysis component and a public education component. This report outlines the work completed since the inception of the project and describes the activities still in progress.

  3. Update of AMmtDB: a database of multi-aligned metazoa mitochondrial DNA sequences.

    PubMed

    Lanave, C; Attimonelli, M; De Robertis, M; Licciulli, F; Liuni, S; Sbisá, E; Saccone, C

    1999-01-01

    The present paper describes AMmtDB, a database collecting the multi-aligned sequences of vertebrate mitochondrial genes coding for proteins and tRNAs, as well as the multiple alignment of the mammalian mtDNA main regulatory region (D-loop) sequences. The genes coding for proteins are multi-aligned based on the translated sequences and both the nucleotide and amino acid multi-alignments are provided. As far as the genes coding for tRNAs are concerned, the multi-alignments based on the primary and the secondary structures are both provided; for the mammalian D-loop multi-alignments we report the conserved regions of the entire D-loop (CSB1, CSB2, CSB3, the central region, ETAS1 and ETAS2) as defined by Sbisà et al. [ Gene (1997), 205, 125-140). A flatfile format for AMmtDB has been designed allowing its implementation in SRS (http://bio-www.ba.cnr.it:8000/BioWWW/#AMMTDB ). Data selected through SRS can be managed using GeneDoc or other programs for the management of multi-aligned data depending on the user's operative system. The multiple alignments have been produced with CLUSTALV and PILEUP programs and then carefully optimized manually. PMID:9847158

  4. Covariation of the Incidence of Type 1 Diabetes with Country Characteristics Available in Public Databases

    PubMed Central

    Diaz-Valencia, Paula Andrea; Bougnères, Pierre; Valleron, Alain-Jacques

    2015-01-01

    Background The incidence of Type 1 Diabetes (T1D) in children varies dramatically between countries. Part of the explanation must be sought in environmental factors. Increasingly, public databases provide information on country-to-country environmental differences. Methods Information on the incidence of T1D and country characteristics were searched for in the 194 World Health Organization (WHO) member countries. T1D incidence was extracted from a systematic literature review of all papers published between 1975 and 2014, including the 2013 update from the International Diabetes Federation. The information on country characteristics was searched in public databases. We considered all indicators with a plausible relation with T1D and those previously reported as correlated with T1D, and for which there was less than 5% missing values. This yielded 77 indicators. Four domains were explored: Climate and environment, Demography, Economy, and Health Conditions. Bonferroni correction to correct false discovery rate (FDR) was used in bivariate analyses. Stepwise multiple regressions, served to identify independent predictors of the geographical variation of T1D. Findings T1D incidence was estimated for 80 WHO countries. Forty-one significant correlations between T1D and the selected indicators were found. Stepwise Multiple Linear Regressions performed in the four explored domains indicated that the percentages of variance explained by the indicators were respectively 35% for Climate and environment, 33% for Demography, 45% for Economy, and 46% for Health conditions, and 51% in the Final model, where all variables selected by domain were considered. Significant environmental predictors of the country-to-country variation of T1D incidence included UV radiation, number of mobile cellular subscriptions in the country, health expenditure per capita, hepatitis B immunization and mean body mass index (BMI). Conclusions The increasing availability of public databases providing

  5. MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data.

    PubMed

    Zou, Dong; Sun, Shixiang; Li, Rujiao; Liu, Jiang; Zhang, Jing; Zhang, Zhang

    2015-01-01

    DNA methylation plays crucial roles during embryonic development. Here we present MethBank (http://dnamethylome.org), a DNA methylome programming database that integrates the genome-wide single-base nucleotide methylomes of gametes and early embryos in different model organisms. Unlike extant relevant databases, MethBank incorporates the whole-genome single-base-resolution methylomes of gametes and early embryos at multiple different developmental stages in zebrafish and mouse. MethBank allows users to retrieve methylation levels, differentially methylated regions, CpG islands, gene expression profiles and genetic polymorphisms for a specific gene or genomic region. Moreover, it offers a methylome browser that is capable of visualizing high-resolution DNA methylation profiles as well as other related data in an interactive manner and thus is of great helpfulness for users to investigate methylation patterns and changes of gametes and early embryos at different developmental stages. Ongoing efforts are focused on incorporation of methylomes and related data from other organisms. Together, MethBank features integration and visualization of high-resolution DNA methylation data as well as other related data, enabling identification of potential DNA methylation signatures in different developmental stages and accordingly providing an important resource for the epigenetic and developmental studies. PMID:25294826

  6. SBMDb: first whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications.

    PubMed

    Iquebal, Mir Asif; Jaiswal, Sarika; Angadi, U B; Sablok, Gaurav; Arora, Vasu; Kumar, Sunil; Rai, Anil; Kumar, Dinesh

    2015-01-01

    DNA marker plays important role as valuable tools to increase crop productivity by finding plausible answers to genetic variations and linking the Quantitative Trait Loci (QTL) of beneficial trait. Prior approaches in development of Short Tandem Repeats (STR) markers were time consuming and inefficient. Recent methods invoking the development of STR markers using whole genomic or transcriptomics data has gained wide importance with immense potential in developing breeding and cultivator improvement approaches. Availability of whole genome sequences and in silico approaches has revolutionized bulk marker discovery. We report world's first sugarbeet whole genome marker discovery having 145 K markers along with 5 K functional domain markers unified in common platform using MySQL, Apache and PHP in SBMDb. Embedded markers and corresponding location information can be selected for desired chromosome, location/interval and primers can be generated using Primer3 core, integrated at backend. Our analyses revealed abundance of 'mono' repeat (76.82%) over 'di' repeats (13.68%). Highest density (671.05 markers/Mb) was found in chromosome 1 and lowest density (341.27 markers/Mb) in chromosome 6. Current investigation of sugarbeet genome marker density has direct implications in increasing mapping marker density. This will enable present linkage map having marker distance of ∼2 cM, i.e. from 200 to 2.6 Kb, thus facilitating QTL/gene mapping. We also report e-PCR-based detection of 2027 polymorphic markers in panel of five genotypes. These markers can be used for DUS test of variety identification and MAS/GAS in variety improvement program. The present database presents wide source of potential markers for developing and implementing new approaches for molecular breeding required to accelerate industrious use of this crop, especially for sugar, health care products, medicines and color dye. Identified markers will also help in improvement of bioenergy trait of

  7. SBMDb: first whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications

    PubMed Central

    Iquebal, Mir Asif; Jaiswal, Sarika; Angadi, U.B.; Sablok, Gaurav; Arora, Vasu; Kumar, Sunil; Rai, Anil; Kumar, Dinesh

    2015-01-01

    DNA marker plays important role as valuable tools to increase crop productivity by finding plausible answers to genetic variations and linking the Quantitative Trait Loci (QTL) of beneficial trait. Prior approaches in development of Short Tandem Repeats (STR) markers were time consuming and inefficient. Recent methods invoking the development of STR markers using whole genomic or transcriptomics data has gained wide importance with immense potential in developing breeding and cultivator improvement approaches. Availability of whole genome sequences and in silico approaches has revolutionized bulk marker discovery. We report world’s first sugarbeet whole genome marker discovery having 145 K markers along with 5 K functional domain markers unified in common platform using MySQL, Apache and PHP in SBMDb. Embedded markers and corresponding location information can be selected for desired chromosome, location/interval and primers can be generated using Primer3 core, integrated at backend. Our analyses revealed abundance of ‘mono’ repeat (76.82%) over ‘di’ repeats (13.68%). Highest density (671.05 markers/Mb) was found in chromosome 1 and lowest density (341.27 markers/Mb) in chromosome 6. Current investigation of sugarbeet genome marker density has direct implications in increasing mapping marker density. This will enable present linkage map having marker distance of ∼2 cM, i.e. from 200 to 2.6 Kb, thus facilitating QTL/gene mapping. We also report e-PCR-based detection of 2027 polymorphic markers in panel of five genotypes. These markers can be used for DUS test of variety identification and MAS/GAS in variety improvement program. The present database presents wide source of potential markers for developing and implementing new approaches for molecular breeding required to accelerate industrious use of this crop, especially for sugar, health care products, medicines and color dye. Identified markers will also help in improvement of bioenergy trait

  8. Familial searching: a specialist forensic DNA profiling service utilising the National DNA Database to identify unknown offenders via their relatives--the UK experience.

    PubMed

    Maguire, C N; McCallum, L A; Storey, C; Whitaker, J P

    2014-01-01

    The National DNA Database (NDNAD) of England and Wales was established on April 10th 1995. The NDNAD is governed by a variety of legislative instruments that mean that DNA samples can be taken if an individual is arrested and detained in a police station. The biological samples and the DNA profiles derived from them can be used for purposes related to the prevention and detection of crime, the investigation of an offence and for the conduct of a prosecution. Following the South East Asian Tsunami of December 2004, the legislation was amended to allow the use of the NDNAD to assist in the identification of a deceased person or of a body part where death has occurred from natural causes or from a natural disaster. The UK NDNAD now contains the DNA profiles of approximately 6 million individuals representing 9.6% of the UK population. As the science of DNA profiling advanced, the National DNA Database provided a potential resource for increased intelligence beyond the direct matching for which it was originally created. The familial searching service offered to the police by several UK forensic science providers exploits the size and geographic coverage of the NDNAD and the fact that close relatives of an offender may share a significant proportion of that offender's DNA profile and will often reside in close geographic proximity to him or her. Between 2002 and 2011 Forensic Science Service Ltd. (FSS) provided familial search services to support 188 police investigations, 70 of which are still active cases. This technique, which may be used in serious crime cases or in 'cold case' reviews when there are few or no investigative leads, has led to the identification of 41 perpetrators or suspects. In this paper we discuss the processes, utility, and governance of the familial search service in which the NDNAD is searched for close genetic relatives of an offender who has left DNA evidence at a crime scene, but whose DNA profile is not represented within the NDNAD. We

  9. Documentation for the U.S. Geological Survey Public-Supply Database (PSDB): a database of permitted public-supply wells, surface-water intakes, and systems in the United States

    USGS Publications Warehouse

    Price, Curtis V.; Maupin, Molly A.

    2014-01-01

    The purpose of this report is to document the PSDB and explain the methods used to populate and update the data from the SDWIS, State datasets, and map and geospatial imagery. This report describes 3 data tables and 11 domain tables, including field contents, data sources, and relations between tables. Although the PSDB database is not available to the general public, this information should be useful for others who are developing other database systems to store and analyze public-supply system and facility data.

  10. SkyDOT: a publicly accessible variability database, containing multiple sky surveys and real-time data

    SciTech Connect

    Starr, D. L.; Wozniak, P. R.; Vestrand, W. T.

    2002-01-01

    SkyDOT (Sky Database for Objects in Time-Domain) is a Virtual Observatory currently comprised of data from the RAPTOR, ROTSE I, and OGLE I1 survey projects. This makes it a very large time domain database. In addition, the RAPTOR project provides SkyDOT with real-time variability data as well as stereoscopic information. With its web interface, we believe SkyDOT will be a very useful tool for both astronomers, and the public. Our main task has been to construct an efficient relational database containing all existing data, while handling a real-time inflow of data. We also provide a useful web interface allowing easy access to both astronomers and the public. Initially, this server will allow common searches, specific queries, and access to light curves. In the future we will include machine learning classification tools and access to spectral information.

  11. Complementary Value of Databases for Discovery of Scholarly Literature: A User Survey of Online Searching for Publications in Art History

    ERIC Educational Resources Information Center

    Nemeth, Erik

    2010-01-01

    Discovery of academic literature through Web search engines challenges the traditional role of specialized research databases. Creation of literature outside academic presses and peer-reviewed publications expands the content for scholarly research within a particular field. The resulting body of literature raises the question of whether scholars…

  12. Defining new criteria for selection of cell-based intestinal models using publicly available databases

    PubMed Central

    2012-01-01

    Background The criteria for choosing relevant cell lines among a vast panel of available intestinal-derived lines exhibiting a wide range of functional properties are still ill-defined. The objective of this study was, therefore, to establish objective criteria for choosing relevant cell lines to assess their appropriateness as tumor models as well as for drug absorption studies. Results We made use of publicly available expression signatures and cell based functional assays to delineate differences between various intestinal colon carcinoma cell lines and normal intestinal epithelium. We have compared a panel of intestinal cell lines with patient-derived normal and tumor epithelium and classified them according to traits relating to oncogenic pathway activity, epithelial-mesenchymal transition (EMT) and stemness, migratory properties, proliferative activity, transporter expression profiles and chemosensitivity. For example, SW480 represent an EMT-high, migratory phenotype and scored highest in terms of signatures associated to worse overall survival and higher risk of recurrence based on patient derived databases. On the other hand, differentiated HT29 and T84 cells showed gene expression patterns closest to tumor bulk derived cells. Regarding drug absorption, we confirmed that differentiated Caco-2 cells are the model of choice for active uptake studies in the small intestine. Regarding chemosensitivity we were unable to confirm a recently proposed association of chemo-resistance with EMT traits. However, a novel signature was identified through mining of NCI60 GI50 values that allowed to rank the panel of intestinal cell lines according to their drug responsiveness to commonly used chemotherapeutics. Conclusions This study presents a straightforward strategy to exploit publicly available gene expression data to guide the choice of cell-based models. While this approach does not overcome the major limitations of such models, introducing a rank order of selected

  13. Contextual models of clinical publications for enhancing retrieval from full-text databases.

    PubMed Central

    Purcell, G. P.; Shortliffe, E. H.

    1995-01-01

    Conventional methods for retrieving information from the medical literature are imprecise and inefficient. Information retrieval systems employ unmanageable indexing vocabularies or use full-text representations that overwhelm the user with irrelevant information. This paper describes a document representation designed to improve the precision of searching in textual databases without significantly compromising recall. The representation augments simple text word representations with contextual models that reflect recurring semantic themes in clinical publications. Using this representation, a searcher may indicate both the terms of interest and the contexts in which they should occur. The contexts limit the potential interpretations of text words, and thus form the basis for more precise searching. In this paper, we discuss the shortcomings of traditional retrieval systems and describe our context-based representation. Improved retrieval performance with contextual models is illustrated by example, and a more extensive study is proposed. We present an evaluation of the contextual models as an indexing scheme, using a variation of the traditional inter-indexer consistency experiments, and we demonstrate that contextual indexing is reproducible by minimally trained physicians and medical students. PMID:8563412

  14. BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology

    PubMed Central

    Gilson, Michael K.; Liu, Tiqing; Baitaluk, Michael; Nicola, George; Hwang, Linda; Chong, Jenny

    2016-01-01

    BindingDB, www.bindingdb.org, is a publicly accessible database of experimental protein-small molecule interaction data. Its collection of over a million data entries derives primarily from scientific articles and, increasingly, US patents. BindingDB provides many ways to browse and search for data of interest, including an advanced search tool, which can cross searches of multiple query types, including text, chemical structure, protein sequence and numerical affinities. The PDB and PubMed provide links to data in BindingDB, and vice versa; and BindingDB provides links to pathway information, the ZINC catalog of available compounds, and other resources. The BindingDB website offers specialized tools that take advantage of its large data collection, including ones to generate hypotheses for the protein targets bound by a bioactive compound, and for the compounds bound by a new protein of known sequence; and virtual compound screening by maximal chemical similarity, binary kernel discrimination, and support vector machine methods. Specialized data sets are also available, such as binding data for hundreds of congeneric series of ligands, drawn from BindingDB and organized for use in validating drug design methods. BindingDB offers several forms of programmatic access, and comes with extensive background material and documentation. Here, we provide the first update of BindingDB since 2007, focusing on new and unique features and highlighting directions of importance to the field as a whole. PMID:26481362

  15. BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology.

    PubMed

    Gilson, Michael K; Liu, Tiqing; Baitaluk, Michael; Nicola, George; Hwang, Linda; Chong, Jenny

    2016-01-01

    BindingDB, www.bindingdb.org, is a publicly accessible database of experimental protein-small molecule interaction data. Its collection of over a million data entries derives primarily from scientific articles and, increasingly, US patents. BindingDB provides many ways to browse and search for data of interest, including an advanced search tool, which can cross searches of multiple query types, including text, chemical structure, protein sequence and numerical affinities. The PDB and PubMed provide links to data in BindingDB, and vice versa; and BindingDB provides links to pathway information, the ZINC catalog of available compounds, and other resources. The BindingDB website offers specialized tools that take advantage of its large data collection, including ones to generate hypotheses for the protein targets bound by a bioactive compound, and for the compounds bound by a new protein of known sequence; and virtual compound screening by maximal chemical similarity, binary kernel discrimination, and support vector machine methods. Specialized data sets are also available, such as binding data for hundreds of congeneric series of ligands, drawn from BindingDB and organized for use in validating drug design methods. BindingDB offers several forms of programmatic access, and comes with extensive background material and documentation. Here, we provide the first update of BindingDB since 2007, focusing on new and unique features and highlighting directions of importance to the field as a whole. PMID:26481362

  16. Compilation of DNA sequences of Escherichia coli K12: description of the interactive databases ECD and ECDC.

    PubMed Central

    Kröger, M; Wahl, R

    1998-01-01

    We have compiled the DNA sequence data for Escherichia coli K12 available from the GenBank and EMBL data libraries and independently from the literature. We provide the most definitive version of the ECD Escherichia coli database now exclusively via the World Wide Web System (http://susi.bio.uni-giessen.de/ecdc.html ). Our database encloses the completed genome sequence recently published by two competing groups and an assembled set of all elder sequences. The organisation of the database allows precise physical location of each individual gene or regulatory region, even taking into consideration discrepancies in nomenclature. The WWW program allows to the user to branch into the original EMBL and SWISS-PROT datafiles. A number of links to other WWW servers dealing with E. coli is provided. A FASTA and BLAST search may be performed online. Besides the WWW format a flat file version may be obtained via ftp. A number of discrepancies between the two systematic sequence determinations and/or the literature have not yet been resolved. However, our database may serve as a reference source for resolution and/or the assignment of strain difference. PMID:9399797

  17. Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines.

    PubMed

    Rupp, Oliver; Becker, Jennifer; Brinkrolf, Karina; Timmermann, Christina; Borth, Nicole; Pühler, Alfred; Noll, Thomas; Goesmann, Alexander

    2014-01-01

    Chinese hamster ovary (CHO) cell lines represent the most commonly used mammalian expression system for the production of therapeutic proteins. In this context, detailed knowledge of the CHO cell transcriptome might help to improve biotechnological processes conducted by specific cell lines. Nevertheless, very few assembled cDNA sequences of CHO cells were publicly released until recently, which puts a severe limitation on biotechnological research. Two extended annotation systems and web-based tools, one for browsing eukaryotic genomes (GenDBE) and one for viewing eukaryotic transcriptomes (SAMS), were established as the first step towards a publicly usable CHO cell genome/transcriptome analysis platform. This is complemented by the development of a new strategy to assemble the ca. 100 million reads, sequenced from a broad range of diverse transcripts, to a high quality CHO cell transcript set. The cDNA libraries were constructed from different CHO cell lines grown under various culture conditions and sequenced using Roche/454 and Illumina sequencing technologies in addition to sequencing reads from a previous study. Two pipelines to extend and improve the CHO cell line transcripts were established. First, de novo assemblies were carried out with the Trinity and Oases assemblers, using varying k-mer sizes. The resulting contigs were screened for potential CDS using ESTScan. Redundant contigs were filtered out using cd-hit-est. The remaining CDS contigs were re-assembled with CAP3. Second, a reference-based assembly with the TopHat/Cufflinks pipeline was performed, using the recently published draft genome sequence of CHO-K1 as reference. Additionally, the de novo contigs were mapped to the reference genome using GMAP and merged with the Cufflinks assembly using the cuffmerge software. With this approach 28,874 transcripts located on 16,492 gene loci could be assembled. Combining the results of both approaches, 65,561 transcripts were identified for CHO cell lines

  18. A two-locus DNA sequence database for identifying host-specific pathogens and phylogenetic diversity within the Fusarium oxysporum species complex

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An electronically portable two-locus DNA sequence database, comprising partial sequences of the translation elongation factor gene (EF-1a, 634 bp alignment) and nearly complete sequences of the nuclear ribosomal intergenic spacer region (IGS rDNA, 2220 bp alignment) for 850 isolates spanning the phy...

  19. Toward fish and seafood traceability: anchovy species determination in fish products by molecular markers and support through a public domain database.

    PubMed

    Jérôme, Marc; Martinsohn, Jann Thorsten; Ortega, Delphine; Carreau, Philippe; Verrez-Bagnis, Véronique; Mouchel, Olivier

    2008-05-28

    Traceability in the fish food sector plays an increasingly important role for consumer protection and confidence building. This is reflected by the introduction of legislation and rules covering traceability on national and international levels. Although traceability through labeling is well established and supported by respective regulations, monitoring and enforcement of these rules are still hampered by the lack of efficient diagnostic tools. We describe protocols using a direct sequencing method based on 212-274-bp diagnostic sequences derived from species-specific mitochondria DNA cytochrome b, 16S rRNA, and cytochrome oxidase subunit I sequences which can efficiently be applied to unambiguously determine even closely related fish species in processed food products labeled "anchovy". Traceability of anchovy-labeled products is supported by the public online database AnchovyID ( http://anchovyid.jrc.ec.europa.eu), which provided data obtained during our study and tools for analytical purposes. PMID:18452298

  20. Towards standards for data exchange and integration and their impact on a public database such as CEBS (Chemical Effects in Biological Systems)

    SciTech Connect

    Fostel, Jennifer M.

    2008-11-15

    Integration, re-use and meta-analysis of high content study data, typical of DNA microarray studies, can increase its scientific utility. Access to study data and design parameters would enhance the mining of data integrated across studies. However, without standards for which data to include in exchange, and common exchange formats, publication of high content data is time-consuming and often prohibitive. The MGED Society ( (www.mged.org)) was formed in response to the widespread publication of microarray data, and the recognition of the utility of data re-use for meta-analysis. The NIEHS has developed the Chemical Effects in Biological Systems (CEBS) database, which can manage and integrate study data and design from biological and biomedical studies. As community standards are developed for study data and metadata it will become increasingly straightforward to publish high content data in CEBS, where they will be available for meta-analysis. Different exchange formats for study data are being developed: Standard for Exchange of Nonclinical Data (SEND; (www.cdisc.org)); Tox-ML ( (www.Leadscope.com)) and Simple Investigation Formatted Text (SIFT) from the NIEHS. Data integration can be done at the level of conclusions about responsive genes and phenotypes, and this workflow is supported by CEBS. CEBS also integrates raw and preprocessed data within a given platform. The utility and a method for integrating data within and across DNA microarray studies is shown in an example analysis using DrugMatrix data deposited in CEBS by Iconix Pharmaceuticals.

  1. A database of mitochondrial DNA hypervariable regions I and II sequences of individuals from Slovakia.

    PubMed

    Lehocký, Ivan; Baldovic, Marian; Kádasi, Ludevít; Metspalu, Ene

    2008-09-01

    In order to identify polymorphic positions and to determine their frequencies and the frequency of haplotypes in the human mitochondrial control region, two hypervariable regions (HV1 and HV2) of the mitochondrial DNA (mtDNA) of 374 unrelated individuals from Slovakia were amplified and sequenced. Sequence comparison led to the identification of 284 mitochondrial lineages as defined by 163 variable sites. Genetic diversity (GD) was estimated at 0.997 and the probability of two randomly selected individuals from population having identical mtDNA types (random match probability, RMP) for the both regions is 0.60%. PMID:19083829

  2. The TTSMI database: a catalog of triplex target DNA sites associated with genes and regulatory elements in the human genome

    PubMed Central

    Jenjaroenpun, Piroon; Chew, Chee Siang; Yong, Tai Pang; Choowongkomon, Kiattawee; Thammasorn, Wimada; Kuznetsov, Vladimir A.

    2015-01-01

    A triplex target DNA site (TTS), a stretch of DNA that is composed of polypurines, is able to form a triple-helix (triplex) structure with triplex-forming oligonucleotides (TFOs) and is able to influence the site-specific modulation of gene expression and/or the modification of genomic DNA. The co-localization of a genomic TTS with gene regulatory signals and functional genome structures suggests that TFOs could potentially be exploited in antigene strategies for the therapy of cancers and other genetic diseases. Here, we present the TTS Mapping and Integration (TTSMI; http://ttsmi.bii.a-star.edu.sg) database, which provides a catalog of unique TTS locations in the human genome and tools for analyzing the co-localization of TTSs with genomic regulatory sequences and signals that were identified using next-generation sequencing techniques and/or predicted by computational models. TTSMI was designed as a user-friendly tool that facilitates (i) fast searching/filtering of TTSs using several search terms and criteria associated with sequence stability and specificity, (ii) interactive filtering of TTSs that co-localize with gene regulatory signals and non-B DNA structures, (iii) exploration of dynamic combinations of the biological signals of specific TTSs and (iv) visualization of a TTS simultaneously with diverse annotation tracks via the UCSC genome browser. PMID:25324314

  3. The TTSMI database: a catalog of triplex target DNA sites associated with genes and regulatory elements in the human genome.

    PubMed

    Jenjaroenpun, Piroon; Chew, Chee Siang; Yong, Tai Pang; Choowongkomon, Kiattawee; Thammasorn, Wimada; Kuznetsov, Vladimir A

    2015-01-01

    A triplex target DNA site (TTS), a stretch of DNA that is composed of polypurines, is able to form a triple-helix (triplex) structure with triplex-forming oligonucleotides (TFOs) and is able to influence the site-specific modulation of gene expression and/or the modification of genomic DNA. The co-localization of a genomic TTS with gene regulatory signals and functional genome structures suggests that TFOs could potentially be exploited in antigene strategies for the therapy of cancers and other genetic diseases. Here, we present the TTS Mapping and Integration (TTSMI; http://ttsmi.bii.a-star.edu.sg) database, which provides a catalog of unique TTS locations in the human genome and tools for analyzing the co-localization of TTSs with genomic regulatory sequences and signals that were identified using next-generation sequencing techniques and/or predicted by computational models. TTSMI was designed as a user-friendly tool that facilitates (i) fast searching/filtering of TTSs using several search terms and criteria associated with sequence stability and specificity, (ii) interactive filtering of TTSs that co-localize with gene regulatory signals and non-B DNA structures, (iii) exploration of dynamic combinations of the biological signals of specific TTSs and (iv) visualization of a TTS simultaneously with diverse annotation tracks via the UCSC genome browser. PMID:25324314

  4. The electric dipole moment of DNA-binding HU protein calculated by the use of an NMR database.

    PubMed

    Takashima, S; Yamaoka, K

    1999-08-30

    Electric birefringence measurements indicated the presence of a large permanent dipole moment in HU protein-DNA complex. In order to substantiate this observation, numerical computation of the dipole moment of HU protein homodimer was carried out by using NMR protein databases. The dipole moments of globular proteins have hitherto been calculated with X-ray databases and NMR data have never been used before. The advantages of NMR databases are: (a) NMR data are obtained, unlike X-ray databases, using protein solutions. Accordingly, this method eliminates the bothersome question as to the possible alteration of the protein structure due to the transition from the crystalline state to the solution state. This question is particularly important for proteins such as HU protein which has some degree of internal flexibility; (b) the three-dimensional coordinates of hydrogen atoms in protein molecules can be determined with a sufficient resolution and this enables the N-H as well as C = O bond moments to be calculated. Since the NMR database of HU protein from Bacillus stearothermophilus consists of 25 models, the surface charge as well as the core dipole moments were computed for each of these structures. The results of these calculations show that the net permanent dipole moments of HU protein homodimer is approximately 500-530 D (1 D = 3.33 x 10(-30) Cm) at pH 7.5 and 600-630 D at the isoelectric point (pH 10.5). These permanent dipole moments are unusually large for a small protein of the size of 19.5 kDa. Nevertheless, the result of numerical calculations is compatible with the electro-optical observation, confirming a very large dipole moment in this protein. PMID:10483709

  5. Osteoporosis prevention among chronic glucocorticoid users: results from a public health insurance database

    PubMed Central

    Trijau, Sophie; de Lamotte, Gaëlle; Pradel, Vincent; Natali, François; Allaria-Lapierre, Véronique; Coudert, Hervé; Pham, Thao; Sciortino, Vincent; Lafforgue, Pierre

    2016-01-01

    Introduction Long-term glucocorticoid therapy is the leading cause of secondary osteoporosis. The management of glucocorticoid-induced osteoporosis (GIOP) seems to be inadequate in many European countries. Objective To evaluate the rate of screening and treatment of GIOP. Design Information was collected from a national public health-insurance database in our geographic area of Provence-Alpes-Côte-d'Azur and in Corsica, from September 2009 through August 2011. Patients We identified participants aged 15 years and over starting glucocorticoid therapy (≥7.5 mg of prednisone equivalent per day during at least 90 days consecutive). This cohort was compared with an age-matched and sex-matched population that did not receive glucocorticoids. Main outcome measures Bone mass, prescription of bone antiresorptive medication and use of calcium and/or vitamin D treatment. Results We identified 32 812 patients who were prescribed glucocorticoid therapy, yielding 1% prevalence. Incidence of glucocorticoid therapy was 2.8/1000 inhabitants/year. Males represented 44%, the mean age was 58 years. The median prednisone-equivalent dose was 11 mg/day (IQR 9–18 mg/day). 8% underwent bone mass measurement. Calcium and/or vitamin D, and bisphosphonates were prescribed in 18% and 12%, respectively. Results were lower for the control population: 3% underwent bone mass measurement and 3% received bisphosphonate therapy. The rates of osteodensitometry and treatments were higher in women over 55 years of age than in men and women 55 years of age and younger, and also when glucocorticoid therapy was initiated by a rheumatologist versus other physician specialty. Conclusions The management of GIOP remains very inadequate, despite the availability of a statutory health insurance system. Targeted interventions are needed to improve the management of GIOP. PMID:27486526

  6. Leading-edge forensic DNA analyses and the necessity of including crime scene investigators, police officers and technicians in a DNA elimination database.

    PubMed

    Lapointe, Martine; Rogic, Anita; Bourgoin, Sarah; Jolicoeur, Christine; Séguin, Diane

    2015-11-01

    In recent years, sophisticated technology has significantly increased the sensitivity and analytical power of genetic analyses so that very little starting material may now produce viable genetic profiles. This sensitivity however, has also increased the risk of detecting unknown genetic profiles assumed to be that of the perpetrator, yet originate from extraneous sources such as from crime scene workers. These contaminants may mislead investigations, keeping criminal cases active and unresolved for long spans of time. Voluntary submission of DNA samples from crime scene workers is fairly low, therefore we have created a promotional method for our staff elimination database that has resulted in a significant increase in voluntary samples since 2011. Our database enforces privacy safeguards and allows for optional anonymity to all staff members. We also offer information sessions at various police precincts to advise crime scene workers of the importance and success of our staff elimination database. This study, a pioneer in its field, has obtained 327 voluntary submissions from crime scene workers to date, of which 46 individual profiles (14%) have been matched to 58 criminal cases. By implementing our methods and respect for individual privacy, forensic laboratories everywhere may see similar growth and success in explaining unidentified genetic profiles in stagnate criminal cases. PMID:26117338

  7. Harmonizing Databases? Using a Quasi-Experimental Design to Evaluate a Public Mental Health Re-entry Program1

    PubMed Central

    Deng, Xiaogang; Fisher, William; Fulwiler, Carl; Sambamoorthi, Usha; Johnson, Craig; Pinals, Debra A.; Sampson, Lisa; Siegfriedt, Julianne

    2012-01-01

    Our study is the first-ever initiative to merge administrative databases in Massachusetts to evaluate an important public mental health program. It examines post-incarceration outcomes of adults with serious mental illness (SMI) enrolled in the Massachusetts Department of Mental Health (DMH) Forensic Transition Team (FTT) program. The program began in 1998 with the goal of transitioning offenders with SMI released from state and local correctional facilities utilizing a core set of transition activities. In this study we evaluate the program’s effectiveness using merged administrative data from various state agencies for the years 2007 – 2011, comparing FTT clients to released prisoners who, despite having serious mental health disorders, did not meet the criterion for DMH services. By systematically describing our original study design and the barriers we encountered, this report will inform future efforts to evaluate public programs using merged administrative databases and electronic health records. PMID:22436598

  8. Data on publications, structural analyses, and queries used to build and utilize the AlloRep database.

    PubMed

    Sousa, Filipa L; Parente, Daniel J; Hessman, Jacob A; Chazelle, Allen; Teichmann, Sarah A; Swint-Kruse, Liskin

    2016-09-01

    The AlloRep database (www.AlloRep.org) (Sousa et al., 2016) [1] compiles extensive sequence, mutagenesis, and structural information for the LacI/GalR family of transcription regulators. Sequence alignments are presented for >3000 proteins in 45 paralog subfamilies and as a subsampled alignment of the whole family. Phenotypic and biochemical data on almost 6000 mutants have been compiled from an exhaustive search of the literature; citations for these data are included herein. These data include information about oligomerization state, stability, DNA binding and allosteric regulation. Protein structural data for 65 proteins are presented as easily-accessible, residue-contact networks. Finally, this article includes example queries to enable the use of the AlloRep database. See the related article, "AlloRep: a repository of sequence, structural and mutagenesis data for the LacI/GalR transcription regulators" (Sousa et al., 2016) [1]. PMID:27508249

  9. The Human Transcript Database: A Catalogue of Full Length cDNA Inserts

    SciTech Connect

    Bouckk John; Michael McLeod; Kim Worley; Richard Gibbs

    1999-09-10

    The BCM Search Launcher provided improved access to web-based sequence analysis services during the granting period and beyond. The Search Launcher web site grouped analysis procedures by function and provided default parameters that provided reasonable search results for most applications. For instance, most queries were automatically masked for repeat sequences prior to sequence database searches to avoid spurious matches. In addition to the web-based access and arrangements that were made using the functions easier, the BCM Search Launcher provided unique value-added applications like the BEAUTY sequence database search tool that combined information about protein domains and sequence database search results to give an enhanced, more complete picture of the reliability and relative value of the information reported. This enhanced search tool made evaluating search results more straight-forward and consistent. Some of the favorite features of the web site are the sequence utilities and the batch client functionality that allows processing of multiple samples from the command line interface. One measure of the success of the BCM Search Launcher is the number of sites that have adopted the models first developed on the site. The graphic display on the BLAST search from the NCBI web site is one such outgrowth, as is the display of protein domain search results within BLAST search results, and the design of the Biology Workbench application. The logs of usage and comments from users confirm the great utility of this resource.

  10. Database and online map service on unstable rock slopes in Norway - From data perpetuation to public information

    NASA Astrophysics Data System (ADS)

    Oppikofer, Thierry; Nordahl, Bobo; Bunkholt, Halvor; Nicolaisen, Magnus; Jarna, Alexandra; Iversen, Sverre; Hermanns, Reginald L.; Böhme, Martina; Yugsi Molina, Freddy X.

    2015-11-01

    The unstable rock slope database is developed and maintained by the Geological Survey of Norway as part of the systematic mapping of unstable rock slopes in Norway. This mapping aims to detect catastrophic rock slope failures before they occur. More than 250 unstable slopes with post-glacial deformation are detected up to now. The main aims of the unstable rock slope database are (1) to serve as a national archive for unstable rock slopes in Norway; (2) to serve for data collection and storage during field mapping; (3) to provide decision-makers with hazard zones and other necessary information on unstable rock slopes for land-use planning and mitigation; and (4) to inform the public through an online map service. The database is organized hierarchically with a main point for each unstable rock slope to which several feature classes and tables are linked. This main point feature class includes several general attributes of the unstable rock slopes, such as site name, general and geological descriptions, executed works, recommendations, technical parameters (volume, lithology, mechanism and others), displacement rates, possible consequences, as well as hazard and risk classification. Feature classes and tables linked to the main feature class include different scenarios of an unstable rock slope, field observation points, sampling points for dating, displacement measurement stations, lineaments, unstable areas, run-out areas, areas affected by secondary effects, along with tables for hazard and risk classification and URL links to further documentation and references. The database on unstable rock slopes in Norway will be publicly consultable through an online map service. Factsheets with key information on unstable rock slopes can be automatically generated and downloaded for each site. Areas of possible rock avalanche run-out and their secondary effects displayed in the online map service, along with hazard and risk assessments, will become important tools for

  11. The MOSART Database: Linking the SART CORS Clinical Database to the Population-Based Massachusetts PELL Reproductive Public Health Data System

    PubMed Central

    Hoang, Lan; Stern, Judy E.; Diop, Hafsatou; Belanoff, Candice; Declercq, Eugene

    2015-01-01

    Although Assisted Reproductive Technology (ART) births make up 1.6 % of births in the US, the impact of ART on subsequent infant and maternal health is not well understood. Clinical ART treatment records linked to population data would be a powerful tool to study long term outcomes among those treated or not by ART. This paper describes the development of a database intended to accomplish this task. We constructed the Massachusetts Outcomes Study of Assisted Reproductive Technology (MOSART) database by linking the Society of Assisted Reproductive Technologies Clinical Outcomes Reporting System (SART CORS) and the Massachusetts (MA) Pregnancy to Early Life Longitudinal (PELL) data systems for children born to MA resident women at MA hospitals between July 2004 and December 2008. PELL data representing 282,971 individual women and their 334,152 deliveries and 342,035 total births were linked with 48,578 cycles of ART treatment in SART CORS delivered to MA residents or women receiving treatment in MA clinics, representing 18,439 eligible women of whom 9,326 had 10,138 deliveries in this time period. A deterministic five phase linkage algorithm methodology was employed. Linkage results, accuracy, and concordance analyses were examined. We linked 9,092 (89.7 %) SART CORS outcome records to PELL delivery records overall, including 95.0 % among known MA residents treated in MA clinics; 70.8 % with full exact matches. There were minimal differences between matched and unmatched delivery records, except for unknown residency and out-of-state ART site. There was very low concordance of reported use of ART treatment between SART CORS and PELL (birth certificate) data. A total of 3.4 % of MA children (11,729) were identified from ART assisted pregnancies (6,556 singletons; 5,173 multiples). The MOSART linked database provides a strong basis for further longitudinal ART outcomes studies and supports the continued development of potentially powerful linked clinical-public health

  12. Update of AMmtDB: a database of multi-aligned metazoa mitochondrial DNA sequences.

    PubMed

    Lanave, C; Liuni, S; Licciulli, F; Attimonelli, M

    2000-01-01

    The AMmtDB database (http://bio-www.ba.cnr.it:8000/srs6/ ) has been updated by collecting the multi-aligned sequences of Chordata mitochondrial genes coding for proteins and tRNAs. The genes coding for proteins are multi-aligned based on the translated sequences and both the nucleotide and amino acid multi-alignments are provided. AMmtDB data selected through SRS can be viewed and managed using GeneDoc or other programs for the management of multi-aligned data depending on the user's operative system. The multiple alignments have been produced with CLUSTALW and PILEUP programs and then carefully optimized manually. PMID:10592208

  13. Demographic and experiential correlates of public attitudes towards cell-free fetal DNA screening

    PubMed Central

    Sayres, Lauren C.; Allyse, Megan; Goodspeed, Taylor A.; Cho, Mildred K.

    2014-01-01

    This study seeks to inform clinical application of cell-free fetal DNA (cffDNA) screening as a novel method for prenatal trisomy detection by investigating public attitudes towards this technology and demographic and experiential characteristics related to these attitudes. Two versions of a 25-item survey assessing interest in cffDNA and existing first-trimester combined screening for either trisomy 13 and 18 or trisomy 21 were distributed among 3,164 members of the United States public. Logistic regression was performed to determine variables predictive of interest in screening options. Approximately 47% of respondents expressed an interest in cffDNA screening for trisomy 13, 18, and 21, with a majority interested in cffDNA screening as a stand-alone technique. A significantly greater percent would consider termination of pregnancy following a diagnosis of trisomy 13 or 18 (52%) over one of trisomy 21 (44%). Willingness to consider abortion of an affected pregnancy was the strongest correlate to interest in both cffDNA and first-trimester combined screening, although markedly more respondents expressed an interest in some form of screening (69% and 71%, respectively) than would consider termination. Greater educational attainment, higher income, and insurance coverage predicted interest in cffDNA screening; stronger religious identification also corresponded to decreased interest. Prior experience with disability and genetic testing was associated with increased interest in cffDNA screening. Several of these factors, in addition to advanced age and Asian race, were, in turn, predictive of respondents’ increased willingness to consider post-diagnosis termination of pregnancy. In conclusion, divergent attitudes towards cffDNA screening - and prenatal options more generally – appear correlated with individual socioeconomic and religious backgrounds and experiences with disability and genetic testing. Clinical implementation and counseling for novel prenatal

  14. Discovery of Possible Gene Relationships through the Application of Self-Organizing Maps to DNA Microarray Databases

    PubMed Central

    Chavez-Alvarez, Rocio; Chavoya, Arturo; Mendez-Vazquez, Andres

    2014-01-01

    DNA microarrays and cell cycle synchronization experiments have made possible the study of the mechanisms of cell cycle regulation of Saccharomyces cerevisiae by simultaneously monitoring the expression levels of thousands of genes at specific time points. On the other hand, pattern recognition techniques can contribute to the analysis of such massive measurements, providing a model of gene expression level evolution through the cell cycle process. In this paper, we propose the use of one of such techniques –an unsupervised artificial neural network called a Self-Organizing Map (SOM)–which has been successfully applied to processes involving very noisy signals, classifying and organizing them, and assisting in the discovery of behavior patterns without requiring prior knowledge about the process under analysis. As a test bed for the use of SOMs in finding possible relationships among genes and their possible contribution in some biological processes, we selected 282 S. cerevisiae genes that have been shown through biological experiments to have an activity during the cell cycle. The expression level of these genes was analyzed in five of the most cited time series DNA microarray databases used in the study of the cell cycle of this organism. With the use of SOM, it was possible to find clusters of genes with similar behavior in the five databases along two cell cycles. This result suggested that some of these genes might be biologically related or might have a regulatory relationship, as was corroborated by comparing some of the clusters obtained with SOMs against a previously reported regulatory network that was generated using biological knowledge, such as protein-protein interactions, gene expression levels, metabolism dynamics, promoter binding, and modification, regulation and transport of proteins. The methodology described in this paper could be applied to the study of gene relationships of other biological processes in different organisms. PMID:24699245

  15. Compilation of DNA sequences of Escherichia coli K12: description of the interactive databases ECD and ECDC (update 1996).

    PubMed Central

    Kröger, M; Wahl, R

    1997-01-01

    We have compiled the DNA sequence data forEscherichia coliavailable from the GenBank and EMBL data libraries and independently from the literature. We provide the most definitive version of the ECDEscherichia colidatabase now exclusively via the World Wide Web System: http://susi.bio.uni-giessen.de/usr/local/www/ html/ecdc.html . Our database encloses an assembled set of contiguous sequences. Each of these contigs compiles all available sequence information, including those derived from a variety of elder sequences. The organisation of the database allows precise physical location of each individual gene or regulatory region, even taking into consideration discrepancies in nomenclature. The WWW program allows to branch into the original EMBL and SWISSPROT datafiles. A number of links to other WWW servers is provided. A FASTA and BLAST search may be performed online. Besides the WWW format a flat file version may be obtained via ftp. The ftp version may also be obtained from the EMBL data library as part of the CD-ROM issue of the EMBL sequence database, which is released and updated every 3 months. After deletion of all detected overlaps a total of 3 588 706 individual bp has been determined up to the end of September 1996. This corresponds to a total of 77.09% of the entire E.coli chromosome consisting of approximately 4655 kb. About 479 kb (10.3%) are additionally available from Kyoto (Japan). Another 94 kb (2%) are available, but mapping has not been confirmed. Thus the total may have reached 89.4%. PMID:9016501

  16. Implications for DNA identification arising from an analysis of Australian forensic databases.

    PubMed

    Ayres, Karen L; Chaseling, Janet; Balding, David J

    2002-09-26

    Previous analyses of Australian samples have suggested that populations of the same broad racial group (Caucasian, Asian, Aboriginal) tend to be genetically similar across states. This suggests that a single national Australian database for each such group may be feasible, which would greatly facilitate casework. We have investigated samples drawn from each of these groups in different Australian states, and have quantified the genetic homogeneity across states within each racial group in terms of the "coancestry coefficient" F(ST). In accord with earlier results, we find that F(ST) values, as estimated from these data, are very small for Caucasians and Asians, usually <0.5%. We find that "declared" Aborigines (which includes many with partly Aboriginal genetic heritage) are also genetically similar across states, although they display some differentiation from a "pure" Aboriginal population (almost entirely of Aboriginal genetic heritage). PMID:12243876

  17. Update of AMmtDB: a database of multi-aligned Metazoa mitochondrial DNA sequences

    PubMed Central

    Lanave, Cecilia; Liuni, Sabino; Licciulli, Flavio; Attimonelli, Marcella

    2000-01-01

    The AMmtDB database (http://bio-www.ba.cnr.it:8000/srs6/ ) has been updated by collecting the multi-aligned sequences of Chordata mitochondrial genes coding for proteins and tRNAs. The genes coding for proteins are multi-aligned based on the translated sequences and both the nucleotide and amino acid multi-alignments are provided. AMmtDB data selected through SRS can be viewed and managed using GeneDoc or other programs for the management of multi-aligned data depending on the user’s operative system. The multiple alignments have been produced with CLUSTALW and PILEUP programs and then carefully optimized manually. PMID:10592208

  18. Analysis of isotropic turbulence using a public database and the Web service model, and applications to study subgrid models

    NASA Astrophysics Data System (ADS)

    Meneveau, Charles; Yang, Yunke; Perlman, Eric; Wan, Minpin; Burns, Randal; Szalay, Alex; Chen, Shiyi; Eyink, Gregory

    2008-11-01

    A public database system archiving a direct numerical simulation (DNS) data set of isotropic, forced turbulence is used for studying basic turbulence dynamics. The data set consists of the DNS output on 1024-cubed spatial points and 1024 time-samples spanning about one large-scale turn-over timescale. This complete space-time history of turbulence is accessible to users remotely through an interface that is based on the Web-services model (see http://turbulence.pha.jhu.edu). Users may write and execute analysis programs on their host computers, while the programs make subroutine-like calls that request desired parts of the data over the network. The architecture of the database is briefly explained, as are some of the new functions such as Lagrangian particle tracking and spatial box-filtering. These tools are used to evaluate and compare subgrid stresses and models.

  19. A large database DNA sequence handling program with generalized searching specifications.

    PubMed

    Stockwell, P A

    1982-01-11

    The program described allows for the creation and manipulation of files of DNA sequence data up to very great lengths. The program uses its own paging system to load segments of the sequence into a small internal buffer so that the program does not have excessive memory requirements. The program offers a menu of functions to the user, and has been written to be forgiving of user errors. A code for the generalised specification of bases as a series of groups (i.e. A or T, Purine, etc.) has been devised and can be used in search specifications or in sequence files. Versions of the program have been developed to run with special efficiency under DIGITAL's RT11 operating system or to run under systems with a suitable implementation of FORTRAN VI. PMID:7063398

  20. Distributing the ERIC Database on Compact Disc: A Case History of Private Sector Involvement in the Distribution of Public Sector Data.

    ERIC Educational Resources Information Center

    Brandhorst, Ted

    1987-01-01

    Describes the partnership between the public and private sectors in developing and marketing the ERIC database in CD-ROM format. Particular emphasis is given to the marketing research and protocols of partnership that were developed. (Author/CLB)

  1. BrassicaTED - a public database for utilization of miniature transposable elements in Brassica species

    PubMed Central

    2014-01-01

    Background MITE, TRIM and SINEs are miniature form transposable elements (mTEs) that are ubiquitous and dispersed throughout entire plant genomes. Tens of thousands of members cause insertion polymorphism at both the inter- and intra- species level. Therefore, mTEs are valuable targets and resources for development of markers that can be utilized for breeding, genetic diversity and genome evolution studies. Taking advantage of the completely sequenced genomes of Brassica rapa and B. oleracea, characterization of mTEs and building a curated database are prerequisite to extending their utilization for genomics and applied fields in Brassica crops. Findings We have developed BrassicaTED as a unique web portal containing detailed characterization information for mTEs of Brassica species. At present, BrassicaTED has datasets for 41 mTE families, including 5894 and 6026 members from 20 MITE families, 1393 and 1639 members from 5 TRIM families, 1270 and 2364 members from 16 SINE families in B. rapa and B. oleracea, respectively. BrassicaTED offers different sections to browse structural and positional characteristics for every mTE family. In addition, we have added data on 289 MITE insertion polymorphisms from a survey of seven Brassica relatives. Genes with internal mTE insertions are shown with detailed gene annotation and microarray-based comparative gene expression data in comparison with their paralogs in the triplicated B. rapa genome. This database also includes a novel tool, K BLAST (Karyotype BLAST), for clear visualization of the locations for each member in the B. rapa and B. oleracea pseudo-genome sequences. Conclusions BrassicaTED is a newly developed database of information regarding the characteristics and potential utility of mTEs including MITE, TRIM and SINEs in B. rapa and B. oleracea. The database will promote the development of desirable mTE-based markers, which can be utilized for genomics and breeding in Brassica species. BrassicaTED will be a

  2. A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE)

    PubMed Central

    Wu, Tsung-Jung; Shamsaddini, Amirhossein; Pan, Yang; Smith, Krista; Crichton, Daniel J.; Simonyan, Vahan; Mazumder, Raja

    2014-01-01

    Years of sequence feature curation by UniProtKB/Swiss-Prot, PIR-PSD, NCBI-CDD, RefSeq and other database biocurators has led to a rich repository of information on functional sites of genes and proteins. This information along with variation-related annotation can be used to scan human short sequence reads from next-generation sequencing (NGS) pipelines for presence of non-synonymous single-nucleotide variations (nsSNVs) that affect functional sites. This and similar workflows are becoming more important because thousands of NGS data sets are being made available through projects such as The Cancer Genome Atlas (TCGA), and researchers want to evaluate their biomarkers in genomic data. BioMuta, an integrated sequence feature database, provides a framework for automated and manual curation and integration of cancer-related sequence features so that they can be used in NGS analysis pipelines. Sequence feature information in BioMuta is collected from the Catalogue of Somatic Mutations in Cancer (COSMIC), ClinVar, UniProtKB and through biocuration of information available from publications. Additionally, nsSNVs identified through automated analysis of NGS data from TCGA are also included in the database. Because of the petabytes of data and information present in NGS primary repositories, a platform HIVE (High-performance Integrated Virtual Environment) for storing, analyzing, computing and curating NGS data and associated metadata has been developed. Using HIVE, 31 979 nsSNVs were identified in TCGA-derived NGS data from breast cancer patients. All variations identified through this process are stored in a Curated Short Read archive, and the nsSNVs from the tumor samples are included in BioMuta. Currently, BioMuta has 26 cancer types with 13 896 small-scale and 308 986 large-scale study-derived variations. Integration of variation data allows identifications of novel or common nsSNVs that can be prioritized in validation studies. Database URL: BioMuta: http

  3. A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE).

    PubMed

    Wu, Tsung-Jung; Shamsaddini, Amirhossein; Pan, Yang; Smith, Krista; Crichton, Daniel J; Simonyan, Vahan; Mazumder, Raja

    2014-01-01

    Years of sequence feature curation by UniProtKB/Swiss-Prot, PIR-PSD, NCBI-CDD, RefSeq and other database biocurators has led to a rich repository of information on functional sites of genes and proteins. This information along with variation-related annotation can be used to scan human short sequence reads from next-generation sequencing (NGS) pipelines for presence of non-synonymous single-nucleotide variations (nsSNVs) that affect functional sites. This and similar workflows are becoming more important because thousands of NGS data sets are being made available through projects such as The Cancer Genome Atlas (TCGA), and researchers want to evaluate their biomarkers in genomic data. BioMuta, an integrated sequence feature database, provides a framework for automated and manual curation and integration of cancer-related sequence features so that they can be used in NGS analysis pipelines. Sequence feature information in BioMuta is collected from the Catalogue of Somatic Mutations in Cancer (COSMIC), ClinVar, UniProtKB and through biocuration of information available from publications. Additionally, nsSNVs identified through automated analysis of NGS data from TCGA are also included in the database. Because of the petabytes of data and information present in NGS primary repositories, a platform HIVE (High-performance Integrated Virtual Environment) for storing, analyzing, computing and curating NGS data and associated metadata has been developed. Using HIVE, 31 979 nsSNVs were identified in TCGA-derived NGS data from breast cancer patients. All variations identified through this process are stored in a Curated Short Read archive, and the nsSNVs from the tumor samples are included in BioMuta. Currently, BioMuta has 26 cancer types with 13 896 small-scale and 308 986 large-scale study-derived variations. Integration of variation data allows identifications of novel or common nsSNVs that can be prioritized in validation studies. Database URL: BioMuta: http

  4. Database on natural polymorphisms and resistance-related non-synonymous mutations in thymidine kinase and DNA polymerase genes of herpes simplex virus types 1 and 2.

    PubMed

    Sauerbrei, Andreas; Bohn-Wippert, Kathrin; Kaspar, Marisa; Krumbholz, Andi; Karrasch, Matthias; Zell, Roland

    2016-01-01

    The use of genotypic resistance testing of herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) is increasing because the rapid availability of results significantly improves the treatment of severe infections, especially in immunocompromised patients. However, an essential precondition is a broad knowledge of natural polymorphisms and resistance-associated mutations in the thymidine kinase (TK) and DNA polymerase (pol) genes, of which the DNA polymerase (Pol) enzyme is targeted by the highly effective antiviral drugs in clinical use. Thus, this review presents a database of all non-synonymous mutations of TK and DNA pol genes of HSV-1 and HSV-2 whose association with resistance or natural gene polymorphism has been clarified by phenotypic and/or functional assays. In addition, the laboratory methods for verifying natural polymorphisms or resistance mutations are summarized. This database can help considerably to facilitate the interpretation of genotypic resistance findings in clinical HSV-1 and HSV-2 strains. PMID:26433780

  5. Seabird databases and the new paradigm for scientific publication and attribution

    USGS Publications Warehouse

    Hatch, Scott A.

    2010-01-01

    For more than 300 years, the peer-reviewed journal article has been the principal medium for packaging and delivering scientific data. With new tools for managing digital data, a new paradigm is emerging—one that demands open and direct access to data and that enables and rewards a broad-based approach to scientific questions. Ground-breaking papers in the future will increasingly be those that creatively mine and synthesize vast stores of data available on the Internet. This is especially true for conservation science, in which essential data can be readily captured in standard record formats. For seabird professionals, a number of globally shared databases are in the offing, or should be. These databases will capture the salient results of inventories and monitoring, pelagic surveys, diet studies, and telemetry. A number of real or perceived barriers to data sharing exist, but none is insurmountable. Our discipline should take an important stride now by adopting a specially designed markup language for annotating and sharing seabird data.

  6. Automatic detection of lung nodules in computed tomography images: training and validation of algorithms using public research databases

    NASA Astrophysics Data System (ADS)

    Camarlinghi, Niccolò

    2013-09-01

    Lung cancer is one of the main public health issues in developed countries. Lung cancer typically manifests itself as non-calcified pulmonary nodules that can be detected reading lung Computed Tomography (CT) images. To assist radiologists in reading images, researchers started, a decade ago, the development of Computer Aided Detection (CAD) methods capable of detecting lung nodules. In this work, a CAD composed of two CAD subprocedures is presented: , devoted to the identification of parenchymal nodules, and , devoted to the identification of the nodules attached to the pleura surface. Both CADs are an upgrade of two methods previously presented as Voxel Based Neural Approach CAD . The novelty of this paper consists in the massive training using the public research Lung International Database Consortium (LIDC) database and on the implementation of new features for classification with respect to the original VBNA method. Finally, the proposed CAD is blindly validated on the ANODE09 dataset. The result of the validation is a score of 0.393, which corresponds to the average sensitivity of the CAD computed at seven predefined false positive rates: 1/8, 1/4, 1/2, 1, 2, 4, and 8 FP/CT.

  7. Genotyping and interpretation of STR-DNA: Low-template, mixtures and database matches-Twenty years of research and development.

    PubMed

    Gill, Peter; Haned, Hinda; Bleka, Oyvind; Hansson, Oskar; Dørum, Guro; Egeland, Thore

    2015-09-01

    The introduction of Short Tandem Repeat (STR) DNA was a revolution within a revolution that transformed forensic DNA profiling into a tool that could be used, for the first time, to create National DNA databases. This transformation would not have been possible without the concurrent development of fluorescent automated sequencers, combined with the ability to multiplex several loci together. Use of the polymerase chain reaction (PCR) increased the sensitivity of the method to enable the analysis of a handful of cells. The first multiplexes were simple: 'the quad', introduced by the defunct UK Forensic Science Service (FSS) in 1994, rapidly followed by a more discriminating 'six-plex' (Second Generation Multiplex) in 1995 that was used to create the world's first national DNA database. The success of the database rapidly outgrew the functionality of the original system - by the year 2000 a new multiplex of ten-loci was introduced to reduce the chance of adventitious matches. The technology was adopted world-wide, albeit with different loci. The political requirement to introduce pan-European databases encouraged standardisation - the development of European Standard Set (ESS) of markers comprising twelve-loci is the latest iteration. Although development has been impressive, the methods used to interpret evidence have lagged behind. For example, the theory to interpret complex DNA profiles (low-level mixtures), had been developed fifteen years ago, but only in the past year or so, are the concepts starting to be widely adopted. A plethora of different models (some commercial and others non-commercial) have appeared. This has led to a confusing 'debate' about the 'best' to use. The different models available are described along with their advantages and disadvantages. A section discusses the development of national DNA databases, along with details of an associated controversy to estimate the strength of evidence of matches. Current methodology is limited to

  8. Evaluation and utilization as a public health tool of a national molecular epidemiological tuberculosis outbreak database within the United Kingdom from 1997 to 2001.

    PubMed

    Drobniewski, F A; Gibson, A; Ruddy, M; Yates, M D

    2003-05-01

    The aim of this study was to develop a national model and analyze the value of a molecular epidemiological Mycobacterium tuberculosis DNA fingerprint-outbreak database. Incidents were investigated by the United Kingdom PHLS Mycobacterium Reference Unit (MRU) from June 1997 to December 2001, inclusive. A total of 124 incidents involving 972 tuberculosis cases, including 520 patient cultures from referred incidents and 452 patient cultures related to two population studies, were examined by using restriction fragment length polymorphism IS6110 fingerprinting and rapid epidemiological typing. Investigations were divided into the following three categories, reflecting different operational strategies: retrospective passive analysis, retrospective active analysis, and retrospective prospective analysis. The majority of incidents were in the retrospective passive analysis category, i.e., the individual submitting isolates has a suspicion they may be linked. Outbreaks were examined in schools, hospitals, farms, prisons, and public houses, and laboratory cross-contamination events and unusual clinical presentations were investigated. Retrospective active analysis involved a major outbreak centered on a high school. Contact tracing of a teenager with smear-positive pulmonary tuberculosis matched 14 individuals, including members of his class, and another 60 cases were identified in schools clinically and radiologically and by skin testing. Retrospective prospective analysis involved an outbreak of 94 isoniazid-resistant tuberculosis cases in London, United Kingdom, that began after cases were identified at one hospital in January 2000. Contact tracing and comparison with MRU databases indicated that the earliest matched case had occurred in 1995. Subsequently, the MRU changed to an active prospective analysis targeting linked isoniazid-monoresistant isolates for follow up. The patients were multiethnic, born mainly in the United Kingdom, and included professionals

  9. DISTRIBUTED STRUCTURE-SEARCHABLE TOXICITY (DSSTOX) DATABASE NETWORK: MAKING PUBLIC TOXICITY DATA RESOURCES MORE ACCESSIBLE AND USABLE FOR DATA EXPLORATION AND SAR DEVELOPMENT

    EPA Science Inventory


    Distributed Structure-Searchable Toxicity (DSSTox) Database Network: Making Public Toxicity Data Resources More Accessible and U sable for Data Exploration and SAR Development

    Many sources of public toxicity data are not currently linked to chemical structure, are not ...

  10. A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions.

    PubMed

    Creighton, Chad J; Nagaraja, Ankur K; Hanash, Samir M; Matzuk, Martin M; Gunaratne, Preethi H

    2008-11-01

    MicroRNAs are short (approximately 22 nucleotides) noncoding RNAs that regulate the stability and translation of mRNA targets. A number of computational algorithms have been developed to help predict which microRNAs are likely to regulate which genes. Gene expression profiling of biological systems where microRNAs might be active can yield hundreds of differentially expressed genes. The commonly used public microRNA target prediction databases facilitate gene-by-gene searches. However, integration of microRNA-mRNA target predictions with gene expression data on a large scale using these databases is currently cumbersome and time consuming for many researchers. We have developed a desktop software application which, for a given target prediction database, retrieves all microRNA:mRNA functional pairs represented by an experimentally derived set of genes. Furthermore, for each microRNA, the software computes an enrichment statistic for overrepresentation of predicted targets within the gene set, which could help to implicate roles for specific microRNAs and microRNA-regulated genes in the system under study. Currently, the software supports searching of results from PicTar, TargetScan, and miRanda algorithms. In addition, the software can accept any user-defined set of gene-to-class associations for searching, which can include the results of other target prediction algorithms, as well as gene annotation or gene-to-pathway associations. A search (using our software) of genes transcriptionally regulated in vitro by estrogen in breast cancer uncovered numerous targeting associations for specific microRNAs-above what could be observed in randomly generated gene lists-suggesting a role for microRNAs in mediating the estrogen response. The software and Excel VBA source code are freely available at http://sigterms.sourceforge.net. PMID:18812437

  11. Creating a data exchange strategy for radiotherapy research: Towards federated databases and anonymised public datasets

    PubMed Central

    Skripcak, Tomas; Belka, Claus; Bosch, Walter; Brink, Carsten; Brunner, Thomas; Budach, Volker; Büttner, Daniel; Debus, Jürgen; Dekker, Andre; Grau, Cai; Gulliford, Sarah; Hurkmans, Coen; Just, Uwe; Krause, Mechthild; Lambin, Philippe; Langendijk, Johannes A.; Lewensohn, Rolf; Lühr, Armin; Maingon, Philippe; Masucci, Michele; Niyazi, Maximilian; Poortmans, Philip; Simon, Monique; Schmidberger, Heinz; Spezi, Emiliano; Stuschke, Martin; Valentini, Vincenzo; Verheij, Marcel; Whitfield, Gillian; Zackrisson, Björn; Zips, Daniel; Baumann, Michael

    2015-01-01

    Disconnected cancer research data management and lack of information exchange about planned and ongoing research are complicating the utilisation of internationally collected medical information for improving cancer patient care. Rapidly collecting/pooling data can accelerate translational research in radiation therapy and oncology. The exchange of study data is one of the fundamental principles behind data aggregation and data mining. The possibilities of reproducing the original study results, performing further analyses on existing research data to generate new hypotheses or developing computational models to support medical decisions (e.g. risk/benefit analysis of treatment options) represent just a fraction of the potential benefits of medical data-pooling. Distributed machine learning and knowledge exchange from federated databases can be considered as one beyond other attractive approaches for knowledge generation within “Big Data”. Data interoperability between research institutions should be the major concern behind a wider collaboration. Information captured in electronic patient records (EPRs) and study case report forms (eCRFs), linked together with medical imaging and treatment planning data, are deemed to be fundamental elements for large multi-centre studies in the field of radiation therapy and oncology. To fully utilise the captured medical information, the study data have to be more than just an electronic version of a traditional (un-modifiable) paper CRF. Challenges that have to be addressed are data interoperability, utilisation of standards, data quality and privacy concerns, data ownership, rights to publish, data pooling architecture and storage. This paper discusses a framework for conceptual packages of ideas focused on a strategic development for international research data exchange in the field of radiation therapy and oncology. PMID:25458128

  12. Creating a data exchange strategy for radiotherapy research: towards federated databases and anonymised public datasets.

    PubMed

    Skripcak, Tomas; Belka, Claus; Bosch, Walter; Brink, Carsten; Brunner, Thomas; Budach, Volker; Büttner, Daniel; Debus, Jürgen; Dekker, Andre; Grau, Cai; Gulliford, Sarah; Hurkmans, Coen; Just, Uwe; Krause, Mechthild; Lambin, Philippe; Langendijk, Johannes A; Lewensohn, Rolf; Lühr, Armin; Maingon, Philippe; Masucci, Michele; Niyazi, Maximilian; Poortmans, Philip; Simon, Monique; Schmidberger, Heinz; Spezi, Emiliano; Stuschke, Martin; Valentini, Vincenzo; Verheij, Marcel; Whitfield, Gillian; Zackrisson, Björn; Zips, Daniel; Baumann, Michael

    2014-12-01

    Disconnected cancer research data management and lack of information exchange about planned and ongoing research are complicating the utilisation of internationally collected medical information for improving cancer patient care. Rapidly collecting/pooling data can accelerate translational research in radiation therapy and oncology. The exchange of study data is one of the fundamental principles behind data aggregation and data mining. The possibilities of reproducing the original study results, performing further analyses on existing research data to generate new hypotheses or developing computational models to support medical decisions (e.g. risk/benefit analysis of treatment options) represent just a fraction of the potential benefits of medical data-pooling. Distributed machine learning and knowledge exchange from federated databases can be considered as one beyond other attractive approaches for knowledge generation within "Big Data". Data interoperability between research institutions should be the major concern behind a wider collaboration. Information captured in electronic patient records (EPRs) and study case report forms (eCRFs), linked together with medical imaging and treatment planning data, are deemed to be fundamental elements for large multi-centre studies in the field of radiation therapy and oncology. To fully utilise the captured medical information, the study data have to be more than just an electronic version of a traditional (un-modifiable) paper CRF. Challenges that have to be addressed are data interoperability, utilisation of standards, data quality and privacy concerns, data ownership, rights to publish, data pooling architecture and storage. This paper discusses a framework for conceptual packages of ideas focused on a strategic development for international research data exchange in the field of radiation therapy and oncology. PMID:25458128

  13. Comparative study of multimodal intra-subject image registration methods on a publicly available database

    NASA Astrophysics Data System (ADS)

    Miri, Mohammad Saleh; Ghayoor, Ali; Johnson, Hans J.; Sonka, Milan

    2016-03-01

    This work reports on a comparative study between five manual and automated methods for intra-subject pair-wise registration of images from different modalities. The study includes a variety of inter-modal image registrations (MR-CT, PET-CT, PET-MR) utilizing different methods including two manual point-based techniques using rigid and similarity transformations, one automated point-based approach based on Iterative Closest Point (ICP) algorithm, and two automated intensity-based methods using mutual information (MI) and normalized mutual information (NMI). These techniques were employed for inter-modal registration of brain images of 9 subjects from a publicly available dataset, and the results were evaluated qualitatively via checkerboard images and quantitatively using root mean square error and MI criteria. In addition, for each inter-modal registration, a paired t-test was performed on the quantitative results in order to find any significant difference between the results of the studied registration techniques.

  14. Comparing subjective image quality measurement methods for the creation of public databases

    NASA Astrophysics Data System (ADS)

    Redi, Judith; Liu, Hantao; Alers, Hani; Zunino, Rodolfo; Heynderickx, Ingrid

    2010-01-01

    The Single Stimulus (SS) method is often chosen to collect subjective data testing no-reference objective metrics, as it is straightforward to implement and well standardized. At the same time, it exhibits some drawbacks; spread between different assessors is relatively large, and the measured ratings depend on the quality range spanned by the test samples, hence the results from different experiments cannot easily be merged . The Quality Ruler (QR) method has been proposed to overcome these inconveniences. This paper compares the performance of the SS and QR method for pictures impaired by Gaussian blur. The research goal is, on one hand, to analyze the advantages and disadvantages of both methods for quality assessment and, on the other, to make quality data of blur impaired images publicly available. The obtained results show that the confidence intervals of the QR scores are narrower than those of the SS scores. This indicates that the QR method enhances consistency across assessors. Moreover, QR scores exhibit a higher linear correlation with the distortion applied. In summary, for the purpose of building datasets of subjective quality, the QR approach seems promising from the viewpoint of both consistency and repeatability.

  15. Exploration of Preterm Birth Rates Using the Public Health Exposome Database and Computational Analysis Methods

    PubMed Central

    Kershenbaum, Anne D.; Langston, Michael A.; Levine, Robert S.; Saxton, Arnold M.; Oyana, Tonny J.; Kilbourne, Barbara J.; Rogers, Gary L.; Gittner, Lisaann S.; Baktash, Suzanne H.; Matthews-Juarez, Patricia; Juarez, Paul D.

    2014-01-01

    Recent advances in informatics technology has made it possible to integrate, manipulate, and analyze variables from a wide range of scientific disciplines allowing for the examination of complex social problems such as health disparities. This study used 589 county-level variables to identify and compare geographical variation of high and low preterm birth rates. Data were collected from a number of publically available sources, bringing together natality outcomes with attributes of the natural, built, social, and policy environments. Singleton early premature county birth rate, in counties with population size over 100,000 persons provided the dependent variable. Graph theoretical techniques were used to identify a wide range of predictor variables from various domains, including black proportion, obesity and diabetes, sexually transmitted infection rates, mother’s age, income, marriage rates, pollution and temperature among others. Dense subgraphs (paracliques) representing groups of highly correlated variables were resolved into latent factors, which were then used to build a regression model explaining prematurity (R-squared = 76.7%). Two lists of counties with large positive and large negative residuals, indicating unusual prematurity rates given their circumstances, may serve as a starting point for ways to intervene and reduce health disparities for preterm births. PMID:25464130

  16. Production of Arrayed and Rearrayed cDNA Libraries for Public Use

    SciTech Connect

    Rasmussen, K

    2005-08-29

    Researchers studying genes and their protein products need an easily available source for that gene. The I.M.A.G.E. Consortium at Lawrence Livermore National Laboratory is an important source of such genes in the form of arrayed cDNA libraries. The arrayed clones and associated data are available to the public, free of restriction. Libraries are transformed and titered into 384-well master plates, from which 2-8 copies are made. One copy plate is stored by LLNL while others are sent to sequencing groups, plate distributors, and to the group which contributed the library. Clones found to be unique and/or full-length are rearrayed and also made publicly available. Bioinformatics tools supporting the use of I.M.A.G.E. clones are accessible via the World Wide Web.

  17. Does language matter? A case study of epidemiological and public health journals, databases and professional education in French, German and Italian.

    PubMed

    Baussano, Iacopo; Brzoska, Patrick; Fedeli, Ugo; Larouche, Claudia; Razum, Oliver; Fung, Isaac C-H

    2008-01-01

    Epidemiology and public health are usually context-specific. Journals published in different languages and countries play a role both as sources of data and as channels through which evidence is incorporated into local public health practice. Databases in these languages facilitate access to relevant journals, and professional education in these languages facilitates the growth of native expertise in epidemiology and public health. However, as English has become the lingua franca of scientific communication in the era of globalisation, many journals published in non-English languages face the difficult dilemma of either switching to English and competing internationally, or sticking to the native tongue and having a restricted circulation among a local readership. This paper discusses the historical development of epidemiology and the current scene of epidemiological and public health journals, databases and professional education in three Western European languages: French, German and Italian, and examines the dynamics and struggles they have today. PMID:18826570

  18. Does language matter? A case study of epidemiological and public health journals, databases and professional education in French, German and Italian

    PubMed Central

    Baussano, Iacopo; Brzoska, Patrick; Fedeli, Ugo; Larouche, Claudia; Razum, Oliver; Fung, Isaac C-H

    2008-01-01

    Epidemiology and public health are usually context-specific. Journals published in different languages and countries play a role both as sources of data and as channels through which evidence is incorporated into local public health practice. Databases in these languages facilitate access to relevant journals, and professional education in these languages facilitates the growth of native expertise in epidemiology and public health. However, as English has become the lingua franca of scientific communication in the era of globalisation, many journals published in non-English languages face the difficult dilemma of either switching to English and competing internationally, or sticking to the native tongue and having a restricted circulation among a local readership. This paper discusses the historical development of epidemiology and the current scene of epidemiological and public health journals, databases and professional education in three Western European languages: French, German and Italian, and examines the dynamics and struggles they have today. PMID:18826570

  19. Comparative Study of Seven Commercial Kits for Human DNA Extraction from Urine Samples Suitable for DNA Biomarker-Based Public Health Studies

    PubMed Central

    El Bali, Latifa; Diman, Aurélie; Bernard, Alfred; Roosens, Nancy H. C.; De Keersmaecker, Sigrid C. J.

    2014-01-01

    Human genomic DNA extracted from urine could be an interesting tool for large-scale public health studies involving characterization of genetic variations or DNA biomarkers as a result of the simple and noninvasive collection method. These studies, involving many samples, require a rapid, easy, and standardized extraction protocol. Moreover, for practicability, there is a necessity to collect urine at a moment different from the first void and to store it appropriately until analysis. The present study compared seven commercial kits to select the most appropriate urinary human DNA extraction procedure for epidemiological studies. DNA yield has been determined using different quantification methods: two classical, i.e., NanoDrop and PicoGreen, and two species-specific real-time quantitative (q)PCR assays, as DNA extracted from urine contains, besides human, microbial DNA also, which largely contributes to the total DNA yield. In addition, the kits giving a good yield were also tested for the presence of PCR inhibitors. Further comparisons were performed regarding the sampling time and the storage conditions. Finally, as a proof-of-concept, an important gene related to smoking has been genotyped using the developed tools. We could select one well-performing kit for the human DNA extraction from urine suitable for molecular diagnostic real-time qPCR-based assays targeting genetic variations, applicable to large-scale studies. In addition, successful genotyping was possible using DNA extracted from urine stored at −20°C for several months, and an acceptable yield could also be obtained from urine collected at different moments during the day, which is particularly important for public health studies. PMID:25365790

  20. Genome databases

    SciTech Connect

    Courteau, J.

    1991-10-11

    Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts in the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.

  1. E-SovTox: An online database of the main publicly-available sources of toxicity data concerning REACH-relevant chemicals published in the Russian language.

    PubMed

    Sihtmäe, Mariliis; Blinova, Irina; Aruoja, Villem; Dubourguier, Henri-Charles; Legrand, Nicolas; Kahru, Anne

    2010-08-01

    A new open-access online database, E-SovTox, is presented. E-SovTox provides toxicological data for substances relevant to the EU Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH) system, from publicly-available Russian language data sources. The database contains information selected mainly from scientific journals published during the Soviet Union era. The main information source for this database - the journal, Gigiena Truda i Professional'nye Zabolevania [Industrial Hygiene and Occupational Diseases], published between 1957 and 1992 - features acute, but also chronic, toxicity data for numerous industrial chemicals, e.g. for rats, mice, guinea-pigs and rabbits. The main goal of the abovementioned toxicity studies was to derive the maximum allowable concentration limits for industrial chemicals in the occupational health settings of the former Soviet Union. Thus, articles featured in the database include mostly data on LD50 values, skin and eye irritation, skin sensitisation and cumulative properties. Currently, the E-SovTox database contains toxicity data selected from more than 500 papers covering more than 600 chemicals. The user is provided with the main toxicity information, as well as abstracts of these papers in Russian and in English (given as provided in the original publication). The search engine allows cross-searching of the database by the name or CAS number of the compound, and the author of the paper. The E-SovTox database can be used as a decision-support tool by researchers and regulators for the hazard assessment of chemical substances. PMID:20822322

  2. Drinking Water Treatability Database (Database)

    EPA Science Inventory

    The drinking Water Treatability Database (TDB) will provide data taken from the literature on the control of contaminants in drinking water, and will be housed on an interactive, publicly-available USEPA web site. It can be used for identifying effective treatment processes, rec...

  3. The Politics of Information: Building a Relational Database To Support Decision-Making at a Public University.

    ERIC Educational Resources Information Center

    Friedman, Debra; Hoffman, Phillip

    2001-01-01

    Describes creation of a relational database at the University of Washington supporting ongoing academic planning at several levels and affecting the culture of decision making. Addresses getting started; sharing the database; questions, worries, and issues; improving access to high-demand courses; the advising function; management of instructional…

  4. Development of a DNA microarray to detect antimicrobial resistance genes identified in the national center for biotechnology information database

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High density genotyping techniques are needed for investigating antimicrobial resistance especially in the case of multi-drug resistant (MDR) isolates. To achieve this all antimicrobial resistance genes in the NCBI Genbank database were identified by key word searches of sequence annotations and the...

  5. Reflections on a decade of research by ASEAN dental faculties: analysis of publications from ISI-WOS databases from 2000 to 2009.

    PubMed

    Sirisinha, Stitaya; Koontongkaew, Sittichai; Phantumvanit, Prathip; Wittayawuttikul, Ruchareka

    2011-05-01

    This communication analyzed research publications in dentistry in the Institute of Scientific Information Web of Science databases of 10 dental faculties in the Association of South-East Asian Nations (ASEAN) from 2000 to 2009. The term used for the "all-document types" search was "Faculty of Dentistry/College of Dentistry." Abstracts presented at regional meetings were also included in the analysis. The Times Higher Education System QS World University Rankings showed that universities in the region fare poorly in world university rankings. Only the National University of Singapore and Nanyang Technological University appeared in the top 100 in 2009; 19 universities in the region, including Indonesia, Malaysia, the Philippines, Singapore, and Thailand, appeared in the top 500. Data from the databases showed that research publications by dental institutes in the region fall short of their Asian counterparts. Singapore and Thailand are the most active in dental research of the ASEAN countries. PMID:25426599

  6. PFR²: a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution.

    PubMed

    Morard, Raphaël; Darling, Kate F; Mahé, Frédéric; Audic, Stéphane; Ujiié, Yurika; Weiner, Agnes K M; André, Aurore; Seears, Heidi A; Wade, Christopher M; Quillévéré, Frédéric; Douady, Christophe J; Escarguel, Gilles; de Garidel-Thoron, Thibault; Siccha, Michael; Kucera, Michal; de Vargas, Colomban

    2015-11-01

    Planktonic foraminifera (Rhizaria) are ubiquitous marine pelagic protists producing calcareous shells with conspicuous morphology. They play an important role in the marine carbon cycle, and their exceptional fossil record serves as the basis for biochronostratigraphy and past climate reconstructions. A major worldwide sampling effort over the last two decades has resulted in the establishment of multiple large collections of cryopreserved individual planktonic foraminifera samples. Thousands of 18S rDNA partial sequences have been generated, representing all major known morphological taxa across their worldwide oceanic range. This comprehensive data coverage provides an opportunity to assess patterns of molecular ecology and evolution in a holistic way for an entire group of planktonic protists. We combined all available published and unpublished genetic data to build PFR(2), the Planktonic foraminifera Ribosomal Reference database. The first version of the database includes 3322 reference 18S rDNA sequences belonging to 32 of the 47 known morphospecies of extant planktonic foraminifera, collected from 460 oceanic stations. All sequences have been rigorously taxonomically curated using a six-rank annotation system fully resolved to the morphological species level and linked to a series of metadata. The PFR(2) website, available at http://pfr2.sb-roscoff.fr, allows downloading the entire database or specific sections, as well as the identification of new planktonic foraminiferal sequences. Its novel, fully documented curation process integrates advances in morphological and molecular taxonomy. It allows for an increase in its taxonomic resolution and assures that integrity is maintained by including a complete contingency tracking of annotations and assuring that the annotations remain internally consistent. PMID:25828689

  7. BDNF DNA methylation changes as a biomarker of psychiatric disorders: literature review and open access database analysis.

    PubMed

    Zheleznyakova, Galina Y; Cao, Hao; Schiöth, Helgi B

    2016-01-01

    Brain-derived neurotrophic factor (BDNF) plays an important role in nervous system development and function and it is well established that BDNF is involved in the pathogenesis of a wide range of psychiatric disorders. Recently, numerous studies have associated the DNA methylation level of BDNF promoters with certain psychiatric phenotypes. In this review, we summarize data from current literature as well as from our own analysis with respect to the correlation of BDNF methylation changes with psychiatric disorders and address questions about whether DNA methylation related to the BDNF can be useful as biomarker for specific neuropsychiatric disorders. PMID:27267954

  8. DNA.

    ERIC Educational Resources Information Center

    Felsenfeld, Gary

    1985-01-01

    Structural form, bonding scheme, and chromatin structure of and gene-modification experiments with deoxyribonucleic acid (DNA) are described. Indicates that DNA's double helix is variable and also flexible as it interacts with regulatory and other molecules to transfer hereditary messages. (DH)

  9. Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools.

    PubMed

    Cer, Regina Z; Donohue, Duncan E; Mudunuri, Uma S; Temiz, Nuri A; Loss, Michael A; Starner, Nathan J; Halusa, Goran N; Volfovsky, Natalia; Yi, Ming; Luke, Brian T; Bacolla, Albino; Collins, Jack R; Stephens, Robert M

    2013-01-01

    The non-B DB, available at http://nonb.abcc.ncifcrf.gov, catalogs predicted non-B DNA-forming sequence motifs, including Z-DNA, G-quadruplex, A-phased repeats, inverted repeats, mirror repeats, direct repeats and their corresponding subsets: cruciforms, triplexes and slipped structures, in several genomes. Version 2.0 of the database revises and re-implements the motif discovery algorithms to better align with accepted definitions and thresholds for motifs, expands the non-B DNA-forming motifs coverage by including short tandem repeats and adds key visualization tools to compare motif locations relative to other genomic annotations. Non-B DB v2.0 extends the ability for comparative genomics by including re-annotation of the five organisms reported in non-B DB v1.0, human, chimpanzee, dog, macaque and mouse, and adds seven additional organisms: orangutan, rat, cow, pig, horse, platypus and Arabidopsis thaliana. Additionally, the non-B DB v2.0 provides an overall improved graphical user interface and faster query performance. PMID:23125372

  10. MalAvi: a public database of malaria parasites and related haemosporidians in avian hosts based on mitochondrial cytochrome b lineages.

    PubMed

    Bensch, Staffan; Hellgren, Olof; Pérez-Tris, Javier

    2009-09-01

    Research in avian blood parasites has seen a remarkable increase since the introduction of polymerase chain reaction-based methods for parasite identification. New data are revealing complex multihost-multiparasite systems which are difficult to understand without good knowledge of the host range and geographical distribution of the parasite lineages. However, such information is currently difficult to obtain from the literature, or from general repositories such as GenBank, mainly because (i) different research groups use different parasite lineage names, (ii) GenBank entries frequently refer only to the first host and locality at which each parasite was sampled, and (iii) different researchers use different gene fragments to identify parasite lineages. We propose a unified database of avian blood parasites of the genera Plasmodium, Haemoproteus and Leucocytozoon identified by a partial region of their cytochrome b sequences. The database uses a standardized nomenclature to remove synonymy, and concentrates all available information about each parasite in a public reference site, thereby facilitating access to all researchers. Initial data include a list of host species and localities, as well as genetic markers that can be used for phylogenetical analyses. The database is free to download and will be regularly updated by the authors. Prior to publication of new lineages, we encourage researchers to assign names to match the existing database. We anticipate that the value of the database as a source for determining host range and geographical distribution of the parasites will grow with its size and substantially enhance the understanding of this remarkably diverse group of parasites. PMID:21564906

  11. Prevalence of human cell material: DNA and RNA profiling of public and private objects and after activity scenarios.

    PubMed

    van den Berge, M; Ozcanhan, G; Zijlstra, S; Lindenbergh, A; Sijen, T

    2016-03-01

    Especially when minute evidentiary traces are analysed, background cell material unrelated to the crime may contribute to detectable levels in the genetic analyses. To gain understanding on the composition of human cell material residing on surfaces contributing to background traces, we performed DNA and mRNA profiling on samplings of various items. Samples were selected by considering events contributing to cell material deposits in exemplary activities (e.g. dragging a person by the trouser ankles), and can be grouped as public objects, private samples, transfer-related samples and washing machine experiments. Results show that high DNA yields do not necessarily relate to an increased number of contributors or to the detection of other cell types than skin. Background cellular material may be found on any type of public or private item. When a major contributor can be deduced in DNA profiles from private items, this can be a different person than the owner of the item. Also when a specific activity is performed and the areas of physical contact are analysed, the "perpetrator" does not necessarily represent the major contributor in the STR profile. Washing machine experiments show that transfer and persistence during laundry is limited for DNA and cell type dependent for RNA. Skin conditions such as the presence of sebum or sweat can promote DNA transfer. Results of this study, which encompasses 549 samples, increase our understanding regarding the prevalence of human cell material in background and activity scenarios. PMID:26736139

  12. Expanding the forensic German mitochondrial DNA control region database: genetic diversity as a function of sample size and microgeography.

    PubMed

    Pfeiffer, H; Brinkmann, B; Hühne, J; Rolf, B; Morris, A A; Steighner, R; Holland, M M; Forster, P

    1999-01-01

    Mitochondrial DNA control region sequences were determined in 109 unrelated German Caucasoid individuals from north west Germany for both hypervariable regions 1 (HV1) and 2 (HV2) and 100 polymorphic nucleotide positions (nps) were found, 63 in HV1 and 37 in HV2. A total of 100 different mtDNA lineages was revealed, of which 7 were shared by 2 individuals and 1 by 3 individuals. The probability of drawing a HV1 sequence match within the north west Germans or within published sets of south Germans and west Austrians is similar (within a factor of 2) to drawing a sequence match between any two of these three population samples. Furthermore, HV1 sequences of 700 male inhabitants of one village in Lower Saxony were generated and these showed a nearly linear increase of the number of different haplotypes with increasing number of individuals, demonstrating that the commonly used haplotype diversity measure (Nei 1987) for population samples tends to underestimate mtDNA diversity in the actual population. PMID:10460419

  13. Significant variance in genetic diversity among populations of Schistosoma haematobium detected using microsatellite DNA loci from a genome-wide database

    PubMed Central

    2013-01-01

    Background Urogenital schistosomiasis caused by Schistosoma haematobium is widely distributed across Africa and is increasingly being targeted for control. Genome sequences and population genetic parameters can give insight into the potential for population- or species-level drug resistance. Microsatellite DNA loci are genetic markers in wide use by Schistosoma researchers, but there are few primers available for S. haematobium. Methods We sequenced 1,058,114 random DNA fragments from clonal cercariae collected from a snail infected with a single Schistosoma haematobium miracidium. We assembled and aligned the S. haematobium sequences to the genomes of S. mansoni and S. japonicum, identifying microsatellite DNA loci across all three species and designing primers to amplify the loci in S. haematobium. To validate our primers, we screened 32 randomly selected primer pairs with population samples of S. haematobium. Results We designed >13,790 primer pairs to amplify unique microsatellite loci in S. haematobium, (available at http://www.cebio.org/projetos/schistosoma-haematobium-genome). The three Schistosoma genomes contained similar overall frequencies of microsatellites, but the frequency and length distributions of specific motifs differed among species. We identified 15 primer pairs that amplified consistently and were easily scored. We genotyped these 15 loci in S. haematobium individuals from six locations: Zanzibar had the highest levels of diversity; Malawi, Mauritius, Nigeria, and Senegal were nearly as diverse; but the sample from South Africa was much less diverse. Conclusions About half of the primers in the database of Schistosoma haematobium microsatellite DNA loci should yield amplifiable and easily scored polymorphic markers, thus providing thousands of potential markers. Sequence conservation among S. haematobium, S. japonicum, and S. mansoni is relatively high, thus it should now be possible to identify markers that are universal among Schistosoma

  14. Who owns what? Private ownership and the public interest in recombinant DNA technology in the 1970s.

    PubMed

    Yi, Doogab

    2011-09-01

    This essay analyzes how academic institutions, government agencies, and the nascent biotech industry contested the legal ownership of recombinant DNA technology in the name of the public interest. It reconstructs the way a small but influential group of government officials and university research administrators introduced a new framework for the commercialization of academic research in the context of a national debate over scientific research's contributions to American economic prosperity and public health. They claimed that private ownership of inventions arising from public support would provide a powerful means to liberate biomedical discoveries for public benefit. This articulation of the causal link between private ownership and the public interest, it is argued, justified a new set of expectations about the use of research results arising from government or public support, in which commercialization became a new public obligation for academic researchers. By highlighting the broader economic and legal shifts that prompted the reconfiguration of the ownership of public knowledge in late twentieth-century American capitalism, the essay examines the threads of policy-informed legal ideas that came together to affirm private ownership of biomedical knowledge as germane to the public interest in the coming of age of biotechnology and genetic medicine. PMID:22073770

  15. Aviation Safety Issues Database

    NASA Technical Reports Server (NTRS)

    Morello, Samuel A.; Ricks, Wendell R.

    2009-01-01

    The aviation safety issues database was instrumental in the refinement and substantiation of the National Aviation Safety Strategic Plan (NASSP). The issues database is a comprehensive set of issues from an extremely broad base of aviation functions, personnel, and vehicle categories, both nationally and internationally. Several aviation safety stakeholders such as the Commercial Aviation Safety Team (CAST) have already used the database. This broader interest was the genesis to making the database publically accessible and writing this report.

  16. Morchella MLST database

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Welcome to the Morchella MLST database. This dedicated database was set up at the CBS-KNAW Biodiversity Center by Vincent Robert in February 2012, using BioloMICS software (Robert et al., 2011), to facilitate DNA sequence-based identifications of Morchella species via the Internet. The current datab...

  17. The Institute of Public Administration's Document Center: From Paper to Electronic Records--A Full Image Government Documents Database.

    ERIC Educational Resources Information Center

    Al-Zahrani, Rashed S.

    Since its establishment in 1960, the Institute of Public Administration (IPA) in Riyadh, Saudi Arabia has had responsibility for documenting Saudi administrative literature, the official publications of Saudi Arabia, and the literature of regional and international organizations through establishment of the Document Center in 1961. This paper…

  18. DNA

    ERIC Educational Resources Information Center

    Stent, Gunther S.

    1970-01-01

    This history for molecular genetics and its explanation of DNA begins with an analysis of the Golden Jubilee essay papers, 1955. The paper ends stating that the higher nervous system is the one major frontier of biological inquiry which still offers some romance of research. (Author/VW)

  19. Publications

    Cancer.gov

    Information about NCI publications including PDQ cancer information for patients and health professionals, patient-education publications, fact sheets, dictionaries, NCI blogs and newsletters and major reports.

  20. National Vulnerability Database (NVD)

    National Institute of Standards and Technology Data Gateway

    National Vulnerability Database (NVD) (Web, free access)   NVD is a comprehensive cyber security vulnerability database that integrates all publicly available U.S. Government vulnerability resources and provides references to industry resources. It is based on and synchronized with the CVE vulnerability naming standard.

  1. Ionic Liquids Database- (ILThermo)

    National Institute of Standards and Technology Data Gateway

    SRD 147 Ionic Liquids Database- (ILThermo) (Web, free access)   IUPAC Ionic Liquids Database, ILThermo, is a free web research tool that allows users worldwide to access an up-to-date data collection from the publications on experimental investigations of thermodynamic, and transport properties of ionic liquids as well as binary and ternary mixtures containing ionic liquids.

  2. The PNNL Quantitative Infrared Database for Gas-Phase Sensing: A spectral Library for Environmental, Hazmat, and Public Safety Standoff Detection

    SciTech Connect

    Johnson, Timothy J.; Sams, Robert L.; Sharpe, Steven W.; Arthur J. Sedlacek III, Richard Colton, Tuan Vo-Dinh

    2004-03-25

    Pacific Northwest National Laboratory (PNNL) continues to expand its library of quantitative infrared reference spectra for remote sensing. The gas-phase data are recorded at 0.1 cm-1 resolution, with nitrogen pressure broadening to one atmosphere to emulate spectra recorded in the field. It is planned that the PNNL library will consist of approximately 500 vapor-phase spectra associated with the U.S. Department of Energy's environmental, energy, and public safety missions. At present, the database is comprised of approximately 300 infrared spectra, many of which represent highly reactive or toxic species. For the 298 K data, each reported spectrum is in fact a composite spectrum generated by a Beer's law plot (at each wavelength) to typically 12 measured spectra. Recent additions to the database include the vapors of several semi-volatile and non-volatile liquids using an improved dissemination technique for vaporizing the liquid into the nitrogen carrier gas. Experimental and analytical methods are used to remove several known and new artifacts associated with FTIR gas-phase spectroscopy. Details concerning sample preparation and composite spectrum generation are discussed.

  3. The PNNL quantitative infrared database for gas-phase sensing: a spectral library for environmental, hazmat, and public safety standoff detection

    NASA Astrophysics Data System (ADS)

    Johnson, Timothy J.; Sams, Robert L.; Sharpe, Steven W.

    2004-03-01

    Pacific Northwest National Laboratory (PNNL) continues to expand its library of quantitative infrared reference spectra for remote sensing. The gas-phase data are recorded at 0.1 cm-1 resolution, with nitrogen pressure broadening to one atmosphere to emulate spectra recorded in the field. It is planned that the PNNL library will consist of approximately 500 vapor-phase spectra associated with the U.S. Department of Energy"s environmental, energy, and public safety missions. At present, the database is comprised of approximately 300 infrared spectra, many of which represent highly reactive or toxic species. For the 298 K data, each reported spectrum is in fact a composite spectrum generated by a Beer"s law plot (at each wavelength) to typically 12 measured spectra. Recent additions to the database include the vapors of several semi-volatile and non-volatile liquids using an improved dissemination technique for vaporizing the liquid into the nitrogen carrier gas. Experimental and analytical methods are used to remove several known and new artifacts associated with FTIR gas-phase spectroscopy. Details concerning sample preparation and composite spectrum generation are discussed.

  4. The PNNL Quantitative Infrared Database for Gas-Phase Sensing: A Spectral Library for Environmental, Hazmat and Public Safety Standoff Detection

    SciTech Connect

    Johnson, Timothy J.; Sams, Robert L.; Sharpe, Steven W.

    2004-01-01

    Pacific Northwest National Laboratory (PNNL) continues to expand its library of quantitative infrared reference spectra for remote sensing. The gas-phase data are recorded at 0.1 cm-1 resolution, with nitrogen pressure broadening to one atmosphere to emulate spectra recorded in the field. It is planned that the PNNL library will consist of approximately 500 vapor-phase spectra associated with DOE’s environmental, energy, and public safety missions. At present, the database is comprised of approximately 300 infrared spectra, many of which represent highly reactive or toxic species. For the 298 K data, each reported spectrum is in fact a composite spectrum generated by a Beer’s law plot (at each wavelength) to typically 12 measured spectra. Recent additions to the database include the vapors of several semi-volatile and non-volatile liquids using an improved dissemination technique for vaporizing the liquid into the nitrogen carrier gas. Experimental and analytical methods are used to remove several known and new artifacts associated with FTIR gas-phase spectroscopy. Details concerning sample preparation and composite spectrum generation are discussed.

  5. HS3D, A Dataset of Homo Sapiens Splice Regions, and its Extraction Procedure from a Major Public Database

    NASA Astrophysics Data System (ADS)

    Pollastro, Pasquale; Rampone, Salvatore

    The aim of this work is to describe a cleaning procedure of GenBank data, producing material to train and to assess the prediction accuracy of computational approaches for gene characterization. A procedure (GenBank2HS3D) has been defined, producing a dataset (HS3D - Homo Sapiens Splice Sites Dataset) of Homo Sapiens Splice regions extracted from GenBank (Rel.123 at this time). It selects, from the complete GenBank Primate Division, entries of Human Nuclear DNA according with several assessed criteria; then it extracts exons and introns from these entries (actually 4523 + 3802). Donor and acceptor sites are then extracted as windows of 140 nucleotides around each splice site (3799 + 3799). After discarding windows not including canonical GT-AG junctions (65 + 74), including insufficient data (not enough material for a 140 nucleotide window) (686 + 589), including not AGCT bases (29 + 30), and redundant (218 + 226), the remaining windows (2796 + 2880) are reported in the dataset. Finally, windows of false splice sites are selected by searching canonical GT-AG pairs in not splicing positions (271 937 + 332 296). The false sites in a range +/- 60 from a true splice site are marked as proximal. HS3D, release 1.2 at this time, is available at the Web server of the University of Sannio: http://www.sci.unisannio.it/docenti/rampone/.

  6. Publications.

    ERIC Educational Resources Information Center

    Aviation/Space, 1980

    1980-01-01

    Presents a variety of publications available from government and nongovernment sources. The government publications are from the Federal Aviation Administration (FAA) and the National Aeronautics and Space Administration (NASA) and are designed for educators, students, and the public. (Author/SA)

  7. DSSTOX STRUCTURE-SEARCHABLE PUBLIC TOXICITY DATABASE NETWORK: CURRENT PROGRESS AND NEW INITIATIVES TO IMPROVE CHEMO-BIOINFORMATICS CAPABILITIES

    EPA Science Inventory

    The EPA DSSTox website (http://www/epa.gov/nheerl/dsstox) publishes standardized, structure-annotated toxicity databases, covering a broad range of toxicity disciplines. Each DSSTox database features documentation written in collaboration with the source authors and toxicity expe...

  8. Mining SNPs from EST databases.

    PubMed

    Picoult-Newberg, L; Ideker, T E; Pohl, M G; Taylor, S L; Donaldson, M A; Nickerson, D A; Boyce-Jacino, M

    1999-02-01

    There is considerable interest in the discovery and characterization of single nucleotide polymorphisms (SNPs) to enable the analysis of the potential relationships between human genotype and phenotype. Here we present a strategy that permits the rapid discovery of SNPs from publicly available expressed sequence tag (EST) databases. From a set of ESTs derived from 19 different cDNA libraries, we assembled 300,000 distinct sequences and identified 850 mismatches from contiguous EST data sets (candidate SNP sites), without de novo sequencing. Through a polymerase-mediated, single-base, primer extension technique, Genetic Bit Analysis (GBA), we confirmed the presence of a subset of these candidate SNP sites and have estimated the allele frequencies in three human populations with different ethnic origins. Altogether, our approach provides a basis for rapid and efficient regional and genome-wide SNP discovery using data assembled from sequences from different libraries of cDNAs. PMID:10022981

  9. Current research status, databases and application of single nucleotide polymorphism.

    PubMed

    Javed, R; Mukesh

    2010-07-01

    Single Nucleotide Polymorphisms (SNPs) are the most frequent form of DNA variation in the genome. SNPs are genetic markers which are bi-allelic in nature and grow at a very fast rate. Current genomic databases contain information on several million SNPs. More than 6 million SNPs have been identified and the information is publicly available through the efforts of the SNP Consortium and others data bases. The NCBI plays a major role in facillating the identification and cataloging of SNPs through creation and maintenance of the public SNP database (dbSNP) by the biomedical community worldwide and stimulate many areas of biological research including the identification of the genetic components of disease. In this review article, we are compiling the existing SNP databases, research status and their application. PMID:21717869

  10. Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

    SciTech Connect

    Omenn, Gilbert; States, David J.; Adamski, Marcin; Blackwell, Thomas W.; Menon, Rajasree; Hermjakob, Henning; Apweiler, Rolf; Haab, Brian B.; Simpson, Richard; Eddes, James; Kapp, Eugene; Moritz, Rod; Chan, Daniel W.; Rai, Alex J.; Admon, Arie; Aebersold, Ruedi; Eng, Jimmy K.; Hancock, William S.; Hefta, Stanley A.; Meyer, Helmut; Paik, Young-Ki; Yoo, Jong-Shin; Ping, Peipei; Pounds, Joel G.; Adkins, Joshua N.; Qian, Xiaohong; Wang, Rong; Wasinger, Valerie; Wu, Chi Yue; Zhao, Xiaohang; Zeng, Rong; Archakov, Alexander; Tsugita, Akira; Beer, Ilan; Pandey, Akhilesh; Pisano, Michael; Andrews, Philip; Tammen, Harald; Speicher, David W.; Hanash, Samir M.

    2005-08-13

    HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anticoagulated plasma; and (3) created a publicly-available knowledge base (www.bioinformatics. med.umich.edu/hupo/ppp; www.ebi.ac.uk/pride). Thirty-five participating laboratories in 13 countries submitted datasets. Working groups addressed (a) specimen stability and protein concentrations; (b) protein identifications from 18 MS/MS datasets; (c) independent analyses from raw MS-MS spectra; (d) search engine performance, subproteome analyses, and biological insights; (e) antibody arrays; and (f) direct MS/SELDI analyses. MS-MS datasets had 15 710 different International Protein Index (IPI) protein IDs; our integration algorithm applied to multiple matches of peptide sequences yielded 9504 IPI proteins identified with one or more peptides and 3020 proteins identified with two or more peptides (the Core Dataset). These proteins have been characterized with Gene Ontology, InterPro, Novartis Atlas, OMIM, and immunoassay based concentration determinations. The database permits examination of many other subsets, such as 1274 proteins identified with three or more peptides. Reverse protein to DNA matching identified proteins for 118 previously unidentified ORFs. We recommend use of plasma instead of serum, with EDTA (or citrate) for anticoagulation. To improve resolution, sensitivity and reproducibility of peptide identifications and protein matches, we recommend combinations of depletion, fractionation, and MS/MS technologies, with explicit criteria for evaluation of spectra, use of search algorithms, and integration of homologous protein matches. This Special Issue of PROTEOMICS presents papers integral to the collaborative analysis plus many reports of supplementary work on various aspects of the PPP workplan

  11. Biofuel Database

    National Institute of Standards and Technology Data Gateway

    Biofuel Database (Web, free access)   This database brings together structural, biological, and thermodynamic data for enzymes that are either in current use or are being considered for use in the production of biofuels.

  12. A practical tool for public health surveillance: Semi-automated coding of short injury narratives from large administrative databases using Naïve Bayes algorithms.

    PubMed

    Marucci-Wellman, Helen R; Lehto, Mark R; Corns, Helen L

    2015-11-01

    Public health surveillance programs in the U.S. are undergoing landmark changes with the availability of electronic health records and advancements in information technology. Injury narratives gathered from hospital records, workers compensation claims or national surveys can be very useful for identifying antecedents to injury or emerging risks. However, classifying narratives manually can become prohibitive for large datasets. The purpose of this study was to develop a human-machine system that could be relatively easily tailored to routinely and accurately classify injury narratives from large administrative databases such as workers compensation. We used a semi-automated approach based on two Naïve Bayesian algorithms to classify 15,000 workers compensation narratives into two-digit Bureau of Labor Statistics (BLS) event (leading to injury) codes. Narratives were filtered out for manual review if the algorithms disagreed or made weak predictions. This approach resulted in an overall accuracy of 87%, with consistently high positive predictive values across all two-digit BLS event categories including the very small categories (e.g., exposure to noise, needle sticks). The Naïve Bayes algorithms were able to identify and accurately machine code most narratives leaving only 32% (4853) for manual review. This strategy substantially reduces the need for resources compared with manual review alone. PMID:26412196

  13. Method and system for normalizing biometric variations to authenticate users from a public database and that ensures individual biometric data privacy

    DOEpatents

    Strait, Robert S.; Pearson, Peter K.; Sengupta, Sailes K.

    2000-01-01

    A password system comprises a set of codewords spaced apart from one another by a Hamming distance (HD) that exceeds twice the variability that can be projected for a series of biometric measurements for a particular individual and that is less than the HD that can be encountered between two individuals. To enroll an individual, a biometric measurement is taken and exclusive-ORed with a random codeword to produce a "reference value." To verify the individual later, a biometric measurement is taken and exclusive-ORed with the reference value to reproduce the original random codeword or its approximation. If the reproduced value is not a codeword, the nearest codeword to it is found, and the bits that were corrected to produce the codeword to it is found, and the bits that were corrected to produce the codeword are also toggled in the biometric measurement taken and the codeword generated during enrollment. The correction scheme can be implemented by any conventional error correction code such as Reed-Muller code R(m,n). In the implementation using a hand geometry device an R(2,5) code has been used in this invention. Such codeword and biometric measurement can then be used to see if the individual is an authorized user. Conventional Diffie-Hellman public key encryption schemes and hashing procedures can then be used to secure the communications lines carrying the biometric information and to secure the database of authorized users.

  14. Computational tools and resources for metabolism-related property predictions. 1. Overview of publicly available (free and commercial) databases and software

    PubMed Central

    Peach, Megan L; Zakharov, Alexey V; Liu, Ruifeng; Pugliese, Angelo; Tawa, Gregory; Wallqvist, Anders; Nicklaus, Marc C

    2014-01-01

    Metabolism has been identified as a defining factor in drug development success or failure because of its impact on many aspects of drug pharmacology, including bioavailability, half-life and toxicity. In this article, we provide an outline and descriptions of the resources for metabolism-related property predictions that are currently either freely or commercially available to the public. These resources include databases with data on, and software for prediction of, several end points: metabolite formation, sites of metabolic transformation, binding to metabolizing enzymes and metabolic stability. We attempt to place each tool in historical context and describe, wherever possible, the data it was based on. For predictions of interactions with metabolizing enzymes, we show a typical set of results for a small test set of compounds. Our aim is to give a clear overview of the areas and aspects of metabolism prediction in which the currently available resources are useful and accurate, and the areas in which they are inadequate or missing entirely. PMID:23088273

  15. Electronic Databases.

    ERIC Educational Resources Information Center

    Williams, Martha E.

    1985-01-01

    Presents examples of bibliographic, full-text, and numeric databases. Also discusses how to access these databases online, aids to online retrieval, and several issues and trends (including copyright and downloading, transborder data flow, use of optical disc/videodisc technology, and changing roles in database generation and processing). (JN)

  16. Database Administrator

    ERIC Educational Resources Information Center

    Moore, Pam

    2010-01-01

    The Internet and electronic commerce (e-commerce) generate lots of data. Data must be stored, organized, and managed. Database administrators, or DBAs, work with database software to find ways to do this. They identify user needs, set up computer databases, and test systems. They ensure that systems perform as they should and add people to the…

  17. Public Databases Supporting Computational Toxicology

    EPA Science Inventory

    A major goal of the emerging field of computational toxicology is the development of screening-level models that predict potential toxicity of chemicals from a combination of mechanistic in vitro assay data and chemical structure descriptors. In order to build these models, resea...

  18. Hawaii bibliographic database

    USGS Publications Warehouse

    Wright, T.L.; Takahashi, T.J.

    1998-01-01

    The Hawaii bibliographic database has been created to contain all of the literature, from 1779 to the present, pertinent to the volcanological history of the Hawaiian-Emperor volcanic chain. References are entered in a PC- and Macintosh-compatible EndNote Plus bibliographic database with keywords and abstracts or (if no abstract) with annotations as to content. Keywords emphasize location, discipline, process, identification of new chemical data or age determinations, and type of publication. The database is updated approximately three times a year and is available to upload from an ftp site. The bibliography contained 8460 references at the time this paper was submitted for publication. Use of the database greatly enhances the power and completeness of library searches for anyone interested in Hawaiian volcanism.

  19. Human variation databases

    PubMed Central

    Küntzer, Jan; Eggle, Daniela; Klostermann, Stefan; Burtscher, Helmut

    2010-01-01

    More than 100 000 human genetic variations have been described in various genes that are associated with a wide variety of diseases. Such data provides invaluable information for both clinical medicine and basic science. A number of locus-specific databases have been developed to exploit this huge amount of data. However, the scope, format and content of these databases differ strongly and as no standard for variation databases has yet been adopted, the way data is presented varies enormously. This review aims to give an overview of current resources for human variation data in public and commercial resources. PMID:20639550

  20. Fast decision tree-based method to index large DNA-protein sequence databases using hybrid distributed-shared memory programming model.

    PubMed

    Jaber, Khalid Mohammad; Abdullah, Rosni; Rashid, Nur'Aini Abdul

    2014-01-01

    In recent times, the size of biological databases has increased significantly, with the continuous growth in the number of users and rate of queries; such that some databases have reached the terabyte size. There is therefore, the increasing need to access databases at the fastest rates possible. In this paper, the decision tree indexing model (PDTIM) was parallelised, using a hybrid of distributed and shared memory on resident database; with horizontal and vertical growth through Message Passing Interface (MPI) and POSIX Thread (PThread), to accelerate the index building time. The PDTIM was implemented using 1, 2, 4 and 5 processors on 1, 2, 3 and 4 threads respectively. The results show that the hybrid technique improved the speedup, compared to a sequential version. It could be concluded from results that the proposed PDTIM is appropriate for large data sets, in terms of index building time. PMID:24794073

  1. International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database--the quality controlled standard tool for routine identification of human and animal pathogenic fungi.

    PubMed

    Irinyi, Laszlo; Serena, Carolina; Garcia-Hermoso, Dea; Arabatzis, Michael; Desnos-Ollivier, Marie; Vu, Duong; Cardinali, Gianluigi; Arthur, Ian; Normand, Anne-Cécile; Giraldo, Alejandra; da Cunha, Keith Cassia; Sandoval-Denis, Marcelo; Hendrickx, Marijke; Nishikaku, Angela Satie; de Azevedo Melo, Analy Salles; Merseguel, Karina Bellinghausen; Khan, Aziza; Parente Rocha, Juliana Alves; Sampaio, Paula; da Silva Briones, Marcelo Ribeiro; e Ferreira, Renata Carmona; de Medeiros Muniz, Mauro; Castañón-Olivares, Laura Rosio; Estrada-Barcenas, Daniel; Cassagne, Carole; Mary, Charles; Duan, Shu Yao; Kong, Fanrong; Sun, Annie Ying; Zeng, Xianyu; Zhao, Zuotao; Gantois, Nausicaa; Botterel, Françoise; Robbertse, Barbara; Schoch, Conrad; Gams, Walter; Ellis, David; Halliday, Catriona; Chen, Sharon; Sorrell, Tania C; Piarroux, Renaud; Colombo, Arnaldo L; Pais, Célia; de Hoog, Sybren; Zancopé-Oliveira, Rosely Maria; Taylor, Maria Lucia; Toriello, Conchita; de Almeida Soares, Célia Maria; Delhaes, Laurence; Stubbe, Dirk; Dromer, Françoise; Ranque, Stéphane; Guarro, Josep; Cano-Lira, Jose F; Robert, Vincent; Velegraki, Aristea; Meyer, Wieland

    2015-05-01

    Human and animal fungal pathogens are a growing threat worldwide leading to emerging infections and creating new risks for established ones. There is a growing need for a rapid and accurate identification of pathogens to enable early diagnosis and targeted antifungal therapy. Morphological and biochemical identification methods are time-consuming and require trained experts. Alternatively, molecular methods, such as DNA barcoding, a powerful and easy tool for rapid monophasic identification, offer a practical approach for species identification and less demanding in terms of taxonomical expertise. However, its wide-spread use is still limited by a lack of quality-controlled reference databases and the evolving recognition and definition of new fungal species/complexes. An international consortium of medical mycology laboratories was formed aiming to establish a quality controlled ITS database under the umbrella of the ISHAM working group on "DNA barcoding of human and animal pathogenic fungi." A new database, containing 2800 ITS sequences representing 421 fungal species, providing the medical community with a freely accessible tool at http://www.isham.org/ and http://its.mycologylab.org/ to rapidly and reliably identify most agents of mycoses, was established. The generated sequences included in the new database were used to evaluate the variation and overall utility of the ITS region for the identification of pathogenic fungi at intra-and interspecies level. The average intraspecies variation ranged from 0 to 2.25%. This highlighted selected pathogenic fungal species, such as the dermatophytes and emerging yeast, for which additional molecular methods/genetic markers are required for their reliable identification from clinical and veterinary specimens. PMID:25802363

  2. How Frequently Do the Results from Completed US Clinical Trials Enter the Public Domain? - A Statistical Analysis of the ClinicalTrials.gov Database

    PubMed Central

    Saito, Hiroki; Gill, Christopher J.

    2014-01-01

    Background Achieving transparency in clinical trials, through either publishing results in a journal or posting results to the ClinicalTrials.gov (CTG) web site, is an essential public health good. However, it remains unknown what proportion of completed studies achieve public disclosure of results (PDOR), or what factors explain these differences. Methods We analyzed data from 400 randomly selected studies within the CTG database that had been listed as ‘completed’ and had at least four years in which to disclose results. Using Kaplan-Meier curves, we calculated times from completion to PDOR (defined as publishing the primary outcomes in a journal and/or posting results to CTG), and identified explanatory variables predicting these outcomes using Cox proportional hazards models. Findings Among the 400 clinical trials, 118 (29.5%) failed to achieve PDOR within four years of completion. The median day from study completion to PDOR among 282 studies (70.5%) that achieved PDOR was 602 days (mean 647 days, SD 454 days). Studies were less likely to achieve PDOR if at earlier stages (phase 2 vs. phase 3/4, adjusted HR 0.60, 95% CI 0.47–0.78), if they only included adult subjects (adjusted HR 0.61, 95% CI 0.45–0.83), involved randomization (adjusted HR 0.62, 95% CI 0.46–0.83), or had smaller sample sizes (≤50 subjects vs. >50, adjusted HR 0.60, 95% CI 0.44–0.83). Industry-funded studies were significantly less likely to be published than non-industry or blended studies (adjusted HR 0.49, 95% CI 0.36–0.66). Conclusions A significant proportion of completed studies did not achieve PDOR within the four years of follow-up, particularly smaller studies at earlier stages of development with industry funding. This constitutes reporting bias and threatens the validity of the clinical research literature in the US. PMID:25025477

  3. JICST Factual Database(1)

    NASA Astrophysics Data System (ADS)

    Kurosawa, Shinji

    The outline of JICST factual database (JOIS-F), which JICST has started from January, 1988, and its online service are described in this paper. First, the author mentions the circumstances from 1973, when its planning was started, to the present, and its relation to "Project by Special Coordination Founds for Promoting Science and Technology". Secondly, databases, which are now under development aiming to start its services from fiscal 1988 or fiscal 1989, of DNA, metallic material intensity, crystal structure, chemical substance regulations, and so forth, are described. Lastly, its online service is briefly explained.

  4. Mining SNPs From EST Databases

    PubMed Central

    Picoult-Newberg, Leslie; Ideker, Trey E.; Pohl, Mark G.; Taylor, Scott L.; Donaldson, Miriam A.; Nickerson, Deborah A.; Boyce-Jacino, Michael

    1999-01-01

    There is considerable interest in the discovery and characterization of single nucleotide polymorphisms (SNPs) to enable the analysis of the potential relationships between human genotype and phenotype. Here we present a strategy that permits the rapid discovery of SNPs from publicly available expressed sequence tag (EST) databases. From a set of ESTs derived from 19 different cDNA libraries, we assembled 300,000 distinct sequences and identified 850 mismatches from contiguous EST data sets (candidate SNP sites), without de novo sequencing. Through a polymerase-mediated, single-base, primer extension technique, Genetic Bit Analysis (GBA), we confirmed the presence of a subset of these candidate SNP sites and have estimated the allele frequencies in three human populations with different ethnic origins. Altogether, our approach provides a basis for rapid and efficient regional and genome-wide SNP discovery using data assembled from sequences from different libraries of cDNAs. [The SNPs identified in this study can be found in the National Center of Biotechnology (NCBI) SNP database under submitter handles ORCHID (SNPS-981210-A) and debnick (SNPS-981209-A and SNPS-981209-B).] PMID:10022981

  5. Statistical databases

    SciTech Connect

    Kogalovskii, M.R.

    1995-03-01

    This paper presents a review of problems related to statistical database systems, which are wide-spread in various fields of activity. Statistical databases (SDB) are referred to as databases that consist of data and are used for statistical analysis. Topics under consideration are: SDB peculiarities, properties of data models adequate for SDB requirements, metadata functions, null-value problems, SDB compromise protection problems, stored data compression techniques, and statistical data representation means. Also examined is whether the present Database Management Systems (DBMS) satisfy the SDB requirements. Some actual research directions in SDB systems are considered.

  6. Assessment and integration of publicly available SAGE, cDNA microarray, and oligonucleotide microarray expression data for global coexpression analyses.

    PubMed

    Griffith, Obi L; Pleasance, Erin D; Fulton, Debra L; Oveisi, Mehrdad; Ester, Martin; Siddiqui, Asim S; Jones, Steven J M

    2005-10-01

    Large amounts of gene expression data from several different technologies are becoming available to the scientific community. A common practice is to use these data to calculate global gene coexpression for validation or integration of other "omic" data. To assess the utility of publicly available datasets for this purpose we have analyzed Homo sapiens data from 1202 cDNA microarray experiments, 242 SAGE libraries, and 667 Affymetrix oligonucleotide microarray experiments. The three datasets compared demonstrate significant but low levels of global concordance (rc<0.11). Assessment against Gene Ontology (GO) revealed that all three platforms identify more coexpressed gene pairs with common biological processes than expected by chance. As the Pearson correlation for a gene pair increased it was more likely to be confirmed by GO. The Affymetrix dataset performed best individually with gene pairs of correlation 0.9-1.0 confirmed by GO in 74% of cases. However, in all cases, gene pairs confirmed by multiple platforms were more likely to be confirmed by GO. We show that combining results from different expression platforms increases reliability of coexpression. A comparison with other recently published coexpression studies found similar results in terms of performance against GO but with each method producing distinctly different gene pair lists. PMID:16098712

  7. Maize databases

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This chapter is a succinct overview of maize data held in the species-specific database MaizeGDB (the Maize Genomics and Genetics Database), and selected multi-species data repositories, such as Gramene/Ensembl Plants, Phytozome, UniProt and the National Center for Biotechnology Information (NCBI), ...

  8. Database Manager

    ERIC Educational Resources Information Center

    Martin, Andrew

    2010-01-01

    It is normal practice today for organizations to store large quantities of records of related information as computer-based files or databases. Purposeful information is retrieved by performing queries on the data sets. The purpose of DATABASE MANAGER is to communicate to students the method by which the computer performs these queries. This…

  9. National Ambient Radiation Database

    SciTech Connect

    Dziuban, J.; Sears, R.

    2003-02-25

    The U.S. Environmental Protection Agency (EPA) recently developed a searchable database and website for the Environmental Radiation Ambient Monitoring System (ERAMS) data. This site contains nationwide radiation monitoring data for air particulates, precipitation, drinking water, surface water and pasteurized milk. This site provides location-specific as well as national information on environmental radioactivity across several media. It provides high quality data for assessing public exposure and environmental impacts resulting from nuclear emergencies and provides baseline data during routine conditions. The database and website are accessible at www.epa.gov/enviro/. This site contains (1) a query for the general public which is easy to use--limits the amount of information provided, but includes the ability to graph the data with risk benchmarks and (2) a query for a more technical user which allows access to all of the data in the database, (3) background information on ER AMS.

  10. Data recovery and integration from public databases uncovers transformation-specific transcriptional downregulation of cAMP-PKA pathway-encoding genes

    PubMed Central

    Balestrieri, Chiara; Alberghina, Lilia; Vanoni, Marco; Chiaradonna, Ferdinando

    2009-01-01

    Background The integration of data from multiple genome-wide assays is essential for understanding dynamic spatio-temporal interactions within cells. Such integration, which leads to a more complete view of cellular processes, offers the opportunity to rationalize better the high amount of "omics" data freely available in several public databases. In particular, integration of microarray-derived transcriptome data with other high-throughput analyses (genomic and mutational analysis, promoter analysis) may allow us to unravel transcriptional regulatory networks under a variety of physio-pathological situations, such as the alteration in the cross-talk between signal transduction pathways in transformed cells. Results Here we sequentially apply web-based and statistical tools to a case study: the role of oncogenic activation of different signal transduction pathways in the transcriptional regulation of genes encoding proteins involved in the cAMP-PKA pathway. To this end, we first re-analyzed available genome-wide expression data for genes encoding proteins of the downstream branch of the PKA pathway in normal tissues and human tumor cell lines. Then, in order to identify mutation-dependent transcriptional signatures, we classified cancer cells as a function of their mutational state. The results of such procedure were used as a starting point to analyze the structure of PKA pathway-encoding genes promoters, leading to identification of specific combinations of transcription factor binding sites, which are neatly consistent with available experimental data and help to clarify the relation between gene expression, transcriptional factors and oncogenes in our case study. Conclusions Genome-wide, large-scale "omics" experimental technologies give different, complementary perspectives on the structure and regulatory properties of complex systems. Even the relatively simple, integrated workflow presented here offers opportunities not only for filtering data noise

  11. RiceFOX: A Database of Arabidopsis Mutant Lines Overexpressing Rice Full-Length cDNA that Contains a Wide Range of Trait Information to Facilitate Analysis of Gene Function

    PubMed Central

    Sakurai, Tetsuya; Kondou, Youichi; Akiyama, Kenji; Kurotani, Atsushi; Higuchi, Mieko; Ichikawa, Takanari; Kuroda, Hirofumi; Kusano, Miyako; Mori, Masaki; Saitou, Tsutomu; Sakakibara, Hitoshi; Sugano, Shoji; Suzuki, Makoto; Takahashi, Hideki; Takahashi, Shinya; Takatsuji, Hiroshi; Yokotani, Naoki; Yoshizumi, Takeshi; Saito, Kazuki; Shinozaki, Kazuo; Oda, Kenji; Hirochika, Hirohiko; Matsui, Minami

    2011-01-01

    Identification of gene function is important not only for basic research but also for applied science, especially with regard to improvements in crop production. For rapid and efficient elucidation of useful traits, we developed a system named FOX hunting (Full-length cDNA Over-eXpressor gene hunting) using full-length cDNAs (fl-cDNAs). A heterologous expression approach provides a solution for the high-throughput characterization of gene functions in agricultural plant species. Since fl-cDNAs contain all the information of functional mRNAs and proteins, we introduced rice fl-cDNAs into Arabidopsis plants for systematic gain-of-function mutation. We generated >30,000 independent Arabidopsis transgenic lines expressing rice fl-cDNAs (rice FOX Arabidopsis mutant lines). These rice FOX Arabidopsis lines were screened systematically for various criteria such as morphology, photosynthesis, UV resistance, element composition, plant hormone profile, metabolite profile/fingerprinting, bacterial resistance, and heat and salt tolerance. The information obtained from these screenings was compiled into a database named ‘RiceFOX’. This database contains around 18,000 records of rice FOX Arabidopsis lines and allows users to search against all the observed results, ranging from morphological to invisible traits. The number of searchable items is approximately 100; moreover, the rice FOX Arabidopsis lines can be searched by rice and Arabidopsis gene/protein identifiers, sequence similarity to the introduced rice fl-cDNA and traits. The RiceFOX database is available at http://ricefox.psc.riken.jp/. PMID:21186176

  12. Laboratory information management systems for DNA barcoding.

    PubMed

    Parker, Meaghan; Stones-Havas, Steven; Starger, Craig; Meyer, Christopher

    2012-01-01

    In the field of molecular biology, laboratory information management systems (LIMSs) have been created to track workflows through a process pipeline. For the purposes of DNA barcoding, this workflow involves tracking tissues through extraction, PCR, cycle sequencing, and consensus assembly. Importantly, a LIMS that serves the DNA barcoding community must link required elements for public submissions (e.g., primers, trace files) that are generated in the molecular lab with specimen metadata. Here, we demonstrate an example workflow of a specimen's entry into the LIMS database to the publishing of the specimen's genetic data to a public database using Geneious bioinformatics software. Throughout the process, the connections between steps in the workflow are maintained to facilitate post-processing annotation, structured reporting, and fully transparent edits to reduce subjectivity and increase repeatability. PMID:22684961

  13. Investigating Evolutionary Questions Using Online Molecular Databases.

    ERIC Educational Resources Information Center

    Puterbaugh, Mary N.; Burleigh, J. Gordon

    2001-01-01

    Recommends using online molecular databases as teaching tools to illustrate evolutionary questions and concepts while introducing students to public molecular databases. Provides activities in which students make molecular comparisons between species. (YDS)

  14. USDA NATIONAL NUTRIENT DATABASE FOR STANDARD REFERENCE

    EPA Science Inventory

    The USDA Nutrient Database for Standard Reference (SR) is the major source of food composition data in the United States. It provides the foundation for most food composition databases in the public and private sectors.

  15. IPD: the Immuno Polymorphism Database.

    PubMed

    Robinson, James; Marsh, Steven G E

    2007-01-01

    The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) is a set of specialist databases related to the study of polymorphic genes in the immune system. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of killer cell immunoglobulin-like receptors (KIRs); IPD-MHC, a database of sequences of the major histocompatibility complex (MHC) of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTAB, which provides access to the European Searchable Tumour Cell Line Database, a cell bank of immunologically characterized melanoma cell lines. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. Those sections with similar data, such as IPD-KIR and IPD-MHC, share the same database structure. PMID:18449992

  16. BIOMARKERS DATABASE

    EPA Science Inventory

    This database was developed by assembling and evaluating the literature relevant to human biomarkers. It catalogues and evaluates the usefulness of biomarkers of exposure, susceptibility and effect which may be relevant for a longitudinal cohort study. In addition to describing ...

  17. Fun Databases: My Top Ten.

    ERIC Educational Resources Information Center

    O'Leary, Mick

    1992-01-01

    Provides reviews of 10 online databases: Consumer Reports; Public Opinion Online; Encyclopedia of Associations; Official Airline Guide Adventure Atlas and Events Calendar; CENDATA; Hollywood Hotline; Fearless Taster; Soap Opera Summaries; and Human Sexuality. (LRW)

  18. GaAs Reliability Database

    NASA Technical Reports Server (NTRS)

    Sacco, T.; Gonzalez, S.; Kayali, S.

    1993-01-01

    The database consists of two main sections, the data references and the device reliability records. The reference section contains 8 fields: reference number, date of publication, authors, article title, publisher, volume, and page numbers.

  19. Marmal-aid – a database for Infinium HumanMethylation450

    PubMed Central

    2013-01-01

    Background DNA methylation is indispensible for normal human genome function. Currently there is an increasingly large number of DNA methylomic data being released in the public domain allowing for an opportunity to investigate the relationships between the DNA methylome, genome function, and human phenotypes. The Illumina450K is one of the most popular platforms for assessing DNA methylation with over 10,000 samples available in the public domain. However, accessing all this data requires downloading each individual experiment and due to inconsistent annotation, accessing the right data can be a challenge. Description Here we introduce ‘Marmal-aid’, the first standardised database for DNA methylation (freely available at http://marmal-aid.org). In Marmal-aid, the majority of publicly available Illumina HumanMethylation450 data is incorporated into a single repository allowing for re-processing of data including normalisation and imputation of missing values. The database is accessible in two ways: (1) Using an R package to allow for incorporation into existing analysis pipelines which can then be easily queried to gain insight into the functionality of certain CpG sites. This is aimed at a bioinformatician with experience in R. (2) Using a graphical interface allowing general biologists to query a pre-defined set of tissues (currently 15) providing a reference database of the methylation state in these tissues for the 450,000 CpG sites profiled by the Illumina HumanMethylation450. Conclusion Marmal-aid is the largest publicly available Illumina HumanMethylation450 methylation database combining Illumina HumanMethylation450 data from a number of sources into a single location with a single common annotation format. This allows for automated extraction using the R package and inclusion into existing analysis pipelines. Marmal-aid also provides a easy to use GUI to visualise methylation data in user defined genomic regions for various reference tissues. PMID

  20. Addition of a breeding database in the Genome Database for Rosaceae.

    PubMed

    Evans, Kate; Jung, Sook; Lee, Taein; Brutcher, Lisa; Cho, Ilhyung; Peace, Cameron; Main, Dorrie

    2013-01-01

    Breeding programs produce large datasets that require efficient management systems to keep track of performance, pedigree, geographical and image-based data. With the development of DNA-based screening technologies, more breeding programs perform genotyping in addition to phenotyping for performance evaluation. The integration of breeding data with other genomic and genetic data is instrumental for the refinement of marker-assisted breeding tools, enhances genetic understanding of important crop traits and maximizes access and utility by crop breeders and allied scientists. Development of new infrastructure in the Genome Database for Rosaceae (GDR) was designed and implemented to enable secure and efficient storage, management and analysis of large datasets from the Washington State University apple breeding program and subsequently expanded to fit datasets from other Rosaceae breeders. The infrastructure was built using the software Chado and Drupal, making use of the Natural Diversity module to accommodate large-scale phenotypic and genotypic data. Breeders can search accessions within the GDR to identify individuals with specific trait combinations. Results from Search by Parentage lists individuals with parents in common and results from Individual Variety pages link to all data available on each chosen individual including pedigree, phenotypic and genotypic information. Genotypic data are searchable by markers and alleles; results are linked to other pages in the GDR to enable the user to access tools such as GBrowse and CMap. This breeding database provides users with the opportunity to search datasets in a fully targeted manner and retrieve and compare performance data from multiple selections, years and sites, and to output the data needed for variety release publications and patent applications. The breeding database facilitates efficient program management. Storing publicly available breeding data in a database together with genomic and genetic data will

  1. Addition of a breeding database in the Genome Database for Rosaceae

    PubMed Central

    Evans, Kate; Jung, Sook; Lee, Taein; Brutcher, Lisa; Cho, Ilhyung; Peace, Cameron; Main, Dorrie

    2013-01-01

    Breeding programs produce large datasets that require efficient management systems to keep track of performance, pedigree, geographical and image-based data. With the development of DNA-based screening technologies, more breeding programs perform genotyping in addition to phenotyping for performance evaluation. The integration of breeding data with other genomic and genetic data is instrumental for the refinement of marker-assisted breeding tools, enhances genetic understanding of important crop traits and maximizes access and utility by crop breeders and allied scientists. Development of new infrastructure in the Genome Database for Rosaceae (GDR) was designed and implemented to enable secure and efficient storage, management and analysis of large datasets from the Washington State University apple breeding program and subsequently expanded to fit datasets from other Rosaceae breeders. The infrastructure was built using the software Chado and Drupal, making use of the Natural Diversity module to accommodate large-scale phenotypic and genotypic data. Breeders can search accessions within the GDR to identify individuals with specific trait combinations. Results from Search by Parentage lists individuals with parents in common and results from Individual Variety pages link to all data available on each chosen individual including pedigree, phenotypic and genotypic information. Genotypic data are searchable by markers and alleles; results are linked to other pages in the GDR to enable the user to access tools such as GBrowse and CMap. This breeding database provides users with the opportunity to search datasets in a fully targeted manner and retrieve and compare performance data from multiple selections, years and sites, and to output the data needed for variety release publications and patent applications. The breeding database facilitates efficient program management. Storing publicly available breeding data in a database together with genomic and genetic data will

  2. Experiment Databases

    NASA Astrophysics Data System (ADS)

    Vanschoren, Joaquin; Blockeel, Hendrik

    Next to running machine learning algorithms based on inductive queries, much can be learned by immediately querying the combined results of many prior studies. Indeed, all around the globe, thousands of machine learning experiments are being executed on a daily basis, generating a constant stream of empirical information on machine learning techniques. While the information contained in these experiments might have many uses beyond their original intent, results are typically described very concisely in papers and discarded afterwards. If we properly store and organize these results in central databases, they can be immediately reused for further analysis, thus boosting future research. In this chapter, we propose the use of experiment databases: databases designed to collect all the necessary details of these experiments, and to intelligently organize them in online repositories to enable fast and thorough analysis of a myriad of collected results. They constitute an additional, queriable source of empirical meta-data based on principled descriptions of algorithm executions, without reimplementing the algorithms in an inductive database. As such, they engender a very dynamic, collaborative approach to experimentation, in which experiments can be freely shared, linked together, and immediately reused by researchers all over the world. They can be set up for personal use, to share results within a lab or to create open, community-wide repositories. Here, we provide a high-level overview of their design, and use an existing experiment database to answer various interesting research questions about machine learning algorithms and to verify a number of recent studies.

  3. NUCLEAR DATABASES FOR REACTOR APPLICATIONS.

    SciTech Connect

    PRITYCHENKO, B.; ARCILLA, R.; BURROWS, T.; HERMAN, M.W.; MUGHABGHAB, S.; OBLOZINSKY, P.; ROCHMAN, D.; SONZOGNI, A.A.; TULI, J.; WINCHELL, D.F.

    2006-06-05

    The National Nuclear Data Center (NNDC): An overview of nuclear databases, related products, nuclear data Web services and publications. The NNDC collects, evaluates, and disseminates nuclear physics data for basic research and applied nuclear technologies. The NNDC maintains and contributes to the nuclear reaction (ENDF, CSISRS) and nuclear structure databases along with several others databases (CapGam, MIRD, IRDF-2002) and provides coordination for the Cross Section Evaluation Working Group (CSEWG) and the US Nuclear Data Program (USNDP). The Center produces several publications and codes such as Atlas of Neutron Resonances, Nuclear Wallet Cards booklets and develops codes, such as nuclear reaction model code Empire.

  4. ARTI Refrigerant Database

    SciTech Connect

    Calm, J.M.

    1992-04-30

    The Refrigerant Database consolidates and facilitates access to information to assist industry in developing equipment using alternative refrigerants. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air- conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on R-32, R-123, R-124, R- 125, R-134a, R-141b, R142b, R-143a, R-152a, R-290 (propane), R-717 (ammonia), ethers, and others as well as azeotropic and zeotropic blends of these fluids. It addresses polyalkylene glycol (PAG), ester, and other lubricants. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits.

  5. Solubility Database

    National Institute of Standards and Technology Data Gateway

    SRD 106 IUPAC-NIST Solubility Database (Web, free access)   These solubilities are compiled from 18 volumes (Click here for List) of the International Union for Pure and Applied Chemistry(IUPAC)-NIST Solubility Data Series. The database includes liquid-liquid, solid-liquid, and gas-liquid systems. Typical solvents and solutes include water, seawater, heavy water, inorganic compounds, and a variety of organic compounds such as hydrocarbons, halogenated hydrocarbons, alcohols, acids, esters and nitrogen compounds. There are over 67,500 solubility measurements and over 1800 references.

  6. The Genopolis Microarray Database

    PubMed Central

    Splendiani, Andrea; Brandizi, Marco; Even, Gael; Beretta, Ottavio; Pavelka, Norman; Pelizzola, Mattia; Mayhaus, Manuel; Foti, Maria; Mauri, Giancarlo; Ricciardi-Castagnoli, Paola

    2007-01-01

    Background Gene expression databases are key resources for microarray data management and analysis and the importance of a proper annotation of their content is well understood. Public repositories as well as microarray database systems that can be implemented by single laboratories exist. However, there is not yet a tool that can easily support a collaborative environment where different users with different rights of access to data can interact to define a common highly coherent content. The scope of the Genopolis database is to provide a resource that allows different groups performing microarray experiments related to a common subject to create a common coherent knowledge base and to analyse it. The Genopolis database has been implemented as a dedicated system for the scientific community studying dendritic and macrophage cells functions and host-parasite interactions. Results The Genopolis Database system allows the community to build an object based MIAME compliant annotation of their experiments and to store images, raw and processed data from the Affymetrix GeneChip® platform. It supports dynamical definition of controlled vocabularies and provides automated and supervised steps to control the coherence of data and annotations. It allows a precise control of the visibility of the database content to different sub groups in the community and facilitates exports of its content to public repositories. It provides an interactive users interface for data analysis: this allows users to visualize data matrices based on functional lists and sample characterization, and to navigate to other data matrices defined by similarity of expression values as well as functional characterizations of genes involved. A collaborative environment is also provided for the definition and sharing of functional annotation by users. Conclusion The Genopolis Database supports a community in building a common coherent knowledge base and analyse it. This fills a gap between a local

  7. A comprehensive DNA barcode database for Central European beetles with a focus on Germany: adding more than 3500 identified species to BOLD.

    PubMed

    Hendrich, Lars; Morinière, Jérôme; Haszprunar, Gerhard; Hebert, Paul D N; Hausmann, Axel; Köhler, Frank; Balke, Michael

    2015-07-01

    Beetles are the most diverse group of animals and are crucial for ecosystem functioning. In many countries, they are well established for environmental impact assessment, but even in the well-studied Central European fauna, species identification can be very difficult. A comprehensive and taxonomically well-curated DNA barcode library could remedy this deficit and could also link hundreds of years of traditional knowledge with next generation sequencing technology. However, such a beetle library is missing to date. This study provides the globally largest DNA barcode reference library for Coleoptera for 15 948 individuals belonging to 3514 well-identified species (53% of the German fauna) with representatives from 97 of 103 families (94%). This study is the first comprehensive regional test of the efficiency of DNA barcoding for beetles with a focus on Germany. Sequences ≥500 bp were recovered from 63% of the specimens analysed (15 948 of 25 294) with short sequences from another 997 specimens. Whereas most specimens (92.2%) could be unambiguously assigned to a single known species by sequence diversity at CO1, 1089 specimens (6.8%) were assigned to more than one Barcode Index Number (BIN), creating 395 BINs which need further study to ascertain if they represent cryptic species, mitochondrial introgression, or simply regional variation in widespread species. We found 409 specimens (2.6%) that shared a BIN assignment with another species, most involving a pair of closely allied species as 43 BINs were involved. Most of these taxa were separated by barcodes although sequence divergences were low. Only 155 specimens (0.97%) show identical or overlapping clusters. PMID:25469559

  8. DNA polymerases drive DNA sequencing-by-synthesis technologies: both past and present

    PubMed Central

    Chen, Cheng-Yao

    2014-01-01

    Next-generation sequencing (NGS) technologies have revolutionized modern biological and biomedical research. The engines responsible for this innovation are DNA polymerases; they catalyze the biochemical reaction for deriving template sequence information. In fact, DNA polymerase has been a cornerstone of DNA sequencing from the very beginning. Escherichia coli DNA polymerase I proteolytic (Klenow) fragment was originally utilized in Sanger’s dideoxy chain-terminating DNA sequencing chemistry. From these humble beginnings followed an explosion of organism-specific, genome sequence information accessible via public database. Family A/B DNA polymerases from mesophilic/thermophilic bacteria/archaea were modified and tested in today’s standard capillary electrophoresis (CE) and NGS sequencing platforms. These enzymes were selected for their efficient incorporation of bulky dye-terminator and reversible dye-terminator nucleotides respectively. Third generation, real-time single molecule sequencing platform requires slightly different enzyme properties. Enterobacterial phage ϕ29 DNA polymerase copies long stretches of DNA and possesses a unique capability to efficiently incorporate terminal phosphate-labeled nucleoside polyphosphates. Furthermore, ϕ29 enzyme has also been utilized in emerging DNA sequencing technologies including nanopore-, and protein-transistor-based sequencing. DNA polymerase is, and will continue to be, a crucial component of sequencing technologies. PMID:25009536

  9. DNA data bank of Japan (DDBJ) progress report

    PubMed Central

    Mashima, Jun; Kodama, Yuichi; Kosuge, Takehide; Fujisawa, Takatomo; Katayama, Toshiaki; Nagasaki, Hideki; Okuda, Yoshihiro; Kaminuma, Eli; Ogasawara, Osamu; Okubo, Kousaku; Nakamura, Yasukazu; Takagi, Toshihisa

    2016-01-01

    The DNA Data Bank of Japan Center (DDBJ Center; http://www.ddbj.nig.ac.jp) maintains and provides public archival, retrieval and analytical services for biological information. The contents of the DDBJ databases are shared with the US National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI) within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). Since 2013, the DDBJ Center has been operating the Japanese Genotype-phenotype Archive (JGA) in collaboration with the National Bioscience Database Center (NBDC) in Japan. In addition, the DDBJ Center develops semantic web technologies for data integration and sharing in collaboration with the Database Center for Life Science (DBCLS) in Japan. This paper briefly reports on the activities of the DDBJ Center over the past year including submissions to databases and improvements in our services for data retrieval, analysis, and integration. PMID:26578571

  10. DNA data bank of Japan (DDBJ) progress report.

    PubMed

    Mashima, Jun; Kodama, Yuichi; Kosuge, Takehide; Fujisawa, Takatomo; Katayama, Toshiaki; Nagasaki, Hideki; Okuda, Yoshihiro; Kaminuma, Eli; Ogasawara, Osamu; Okubo, Kousaku; Nakamura, Yasukazu; Takagi, Toshihisa

    2016-01-01

    The DNA Data Bank of Japan Center (DDBJ Center; http://www.ddbj.nig.ac.jp) maintains and provides public archival, retrieval and analytical services for biological information. The contents of the DDBJ databases are shared with the US National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI) within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). Since 2013, the DDBJ Center has been operating the Japanese Genotype-phenotype Archive (JGA) in collaboration with the National Bioscience Database Center (NBDC) in Japan. In addition, the DDBJ Center develops semantic web technologies for data integration and sharing in collaboration with the Database Center for Life Science (DBCLS) in Japan. This paper briefly reports on the activities of the DDBJ Center over the past year including submissions to databases and improvements in our services for data retrieval, analysis, and integration. PMID:26578571